diff options
Diffstat (limited to 'academic/wise')
| -rw-r--r-- | academic/wise/README | 7 | ||||
| -rw-r--r-- | academic/wise/patches/01_welcome-csh.patch | 22 | ||||
| -rw-r--r-- | academic/wise/patches/02_isnumber.patch | 14 | ||||
| -rw-r--r-- | academic/wise/patches/03_doc-nodycache.patch | 15 | ||||
| -rw-r--r-- | academic/wise/patches/04_wise2-pdflatex-update.patch | 38 | ||||
| -rw-r--r-- | academic/wise/patches/05_glib2.patch | 703 | ||||
| -rw-r--r-- | academic/wise/patches/06_getline.patch | 305 | ||||
| -rw-r--r-- | academic/wise/patches/07_ld--as-needed.patch | 52 | ||||
| -rw-r--r-- | academic/wise/patches/08_mayhem.patch | 103 | ||||
| -rw-r--r-- | academic/wise/patches/09_dnal-add-return-statement.patch | 17 | ||||
| -rw-r--r-- | academic/wise/patches/10_fix_path_to_data_files.patch | 337 | ||||
| -rw-r--r-- | academic/wise/patches/11_consistent_manual_dates.patch | 53 | ||||
| -rw-r--r-- | academic/wise/patches/cross.patch | 266 | ||||
| -rw-r--r-- | academic/wise/patches/spelling.patch | 702 | ||||
| -rw-r--r-- | academic/wise/slack-desc | 19 | ||||
| -rw-r--r-- | academic/wise/wise.SlackBuild | 131 | ||||
| -rw-r--r-- | academic/wise/wise.info | 10 |
17 files changed, 2794 insertions, 0 deletions
diff --git a/academic/wise/README b/academic/wise/README new file mode 100644 index 0000000000..6fe23af5ad --- /dev/null +++ b/academic/wise/README @@ -0,0 +1,7 @@ +Wise compares a protein sequence to a genomic DNA sequence, allowing for +introns and frameshifting errors. + +The Wise package is now a rather stately bioinformatics package that has +been around for a while. Its key programs are genewise, a program for +aligning proteins or protein HMMs to DNA, and dynamite a rather cranky +"macro language" which automates the production of dynamic programming. diff --git a/academic/wise/patches/01_welcome-csh.patch b/academic/wise/patches/01_welcome-csh.patch new file mode 100644 index 0000000000..3a9057e062 --- /dev/null +++ b/academic/wise/patches/01_welcome-csh.patch @@ -0,0 +1,22 @@ +Author: Philipp Benner <mail@philipp-benner.de> +Description: Avoid dependency from csh + +--- wise-2.4.1.orig/src/makefile ++++ wise-2.4.1/src/makefile +@@ -109,7 +109,7 @@ + bin : + mkdir bin + cp models/pswdb models/psw models/genewisedb models/estwisedb models/estwise models/genewise models/dba models/dnal models/promoterwise network/scanwise_server models/scanwise ./bin +- csh welcome.csh ++ ./welcome.csh + + libs : + (cd base ; $(MAKE) CC="$(CC)" CFLAGS="$(CFLAGS)" libwisebase.a ) +--- wise-2.4.1.orig/src/welcome.csh ++++ wise-2.4.1/src/welcome.csh +@@ -1,4 +1,4 @@ +-#!/bin/tcsh -f ++#!/bin/sh + + echo "" + echo "Welcome to Wise2.4" diff --git a/academic/wise/patches/02_isnumber.patch b/academic/wise/patches/02_isnumber.patch new file mode 100644 index 0000000000..a6ae90856d --- /dev/null +++ b/academic/wise/patches/02_isnumber.patch @@ -0,0 +1,14 @@ +Author: Philipp Benner <mail@philipp-benner.de> +Description: Replace isnumber() (which does not exist on linux) by isdigit(). + +--- wise-2.4.1.orig/src/models/phasemodel.c ++++ wise-2.4.1/src/models/phasemodel.c +@@ -20,7 +20,7 @@ + if( line[0] == '#' ) { + continue; + } +- if( !isnumber(line[0]) ) { ++ if( !isdigit(line[0]) ) { + warn("Bad looking line in intron file, %s",line); + continue; + } diff --git a/academic/wise/patches/03_doc-nodycache.patch b/academic/wise/patches/03_doc-nodycache.patch new file mode 100644 index 0000000000..6fe7b1893c --- /dev/null +++ b/academic/wise/patches/03_doc-nodycache.patch @@ -0,0 +1,15 @@ +Author Philipp Benner <mail@philipp-benner.de> +Description: Documentation bugfix. + +--- wise-2.4.1.orig/docs/wise2.tex ++++ wise-2.4.1/docs/wise2.tex +@@ -1617,7 +1617,8 @@ + \item[-hithelp] more detailed help on hitlist formats + \item[-dymem] memory style [default/linear/explicit] + \item[-kbyte] memory amount to use [4000] +-\item[-\[no\]dycache] implicitly cache dy matrix usage (default yes) ++\item[-dycache] implicitly cache dy matrix usage (default) ++\item[-nodycache] do not implicitly cache dy matrix usage + \item[-dydebug] drop into dynamite dp matrix debugger + \item[-paldebug] print PackAln after debugger run if used + \item[-help] show help options diff --git a/academic/wise/patches/04_wise2-pdflatex-update.patch b/academic/wise/patches/04_wise2-pdflatex-update.patch new file mode 100644 index 0000000000..bbaf2861d7 --- /dev/null +++ b/academic/wise/patches/04_wise2-pdflatex-update.patch @@ -0,0 +1,38 @@ +Author Philipp Benner <mail@philipp-benner.de> +Description: Make wise2.tex pdflatex compatible. + +--- wise-2.4.1.orig/docs/wise2.tex ++++ wise-2.4.1/docs/wise2.tex +@@ -1,6 +1,7 @@ + + \documentclass{article} +-\usepackage{epsfig} ++%\usepackage{epsfig} ++\usepackage{graphicx} + + \begin{document} + \newcommand{\programtext}[1]{{\tt #1}} +@@ -707,8 +708,9 @@ + \begin{figure} + \begin{center} + \leavevmode +-\epsfxsize 300pt +-\epsfbox{genewise21.eps} ++%\epsfxsize 300pt ++%\epsfbox{genewise21.eps} ++%\includegraphics[scale=0.75]{genewise21.pdf} + \newline + \caption{GeneWise21:93 Algorithm. The dark circles represent states, and the + arrows between them transitions. Black transitions are standard +@@ -898,8 +900,9 @@ + \begin{figure} + \begin{center} + \leavevmode +-\epsfxsize 300pt +-\epsfbox{genewise6.eps} ++%\epsfxsize 300pt ++%\epsfbox{genewise6.eps} ++%\includegraphics[scale=0.75]{genewise6.pdf} + \newline + \caption{GeneWise6:23} + \label{Figure:genewise623} diff --git a/academic/wise/patches/05_glib2.patch b/academic/wise/patches/05_glib2.patch new file mode 100644 index 0000000000..908506524a --- /dev/null +++ b/academic/wise/patches/05_glib2.patch @@ -0,0 +1,703 @@ +Author: Barry deFreese <bdefreese@debian.org> +Description: To build wise2 with the Glib version 2.0 instead of 1.2. +Forwarded: birney@sanger.ac.uk +--- wise-2.4.1.orig/src/makefile ++++ wise-2.4.1/src/makefile +@@ -31,13 +31,13 @@ + + + # Intel icc flags +-# CFLAGS = -c -O3 -axWK -ipo `glib-config --cflags` ++# CFLAGS += -c -axWK -ipo `pkg-config --cflags glib-2.0` + + # alpha flags (-pthread) +-# CFLAGS = -c -O3 -pthread `glib-config --cflags` ++# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0` + + # normal linux/bsd/mac flags +-CFLAGS = -c -O3 `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -c `pkg-config --cflags glib-2.0` + + + EXTRALIBS = -lm +--- wise-2.4.1.orig/src/snp/makefile ++++ wise-2.4.1/src/snp/makefile +@@ -5,9 +5,9 @@ + CC = cc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lpthread -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -16,7 +16,7 @@ + $(CC) $(CFLAGS) $(INCFLAGS) $? + + test_est : test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o +- $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LFLAGS) ++ $(CC) -o test_est test_est.o genotype.o person.o locus_framework.o locus_model_estimators.o frequency_count.o ../dynlibsrc/libdyna.a ../base/libwisebase.a $(LDFLAGS) + + INCFLAGS = -I../base/ -I../dynlibsrc/ + DFLAGS = -l -D -n Wise2_ -a _api.h -b _api.t -pthreads -dbtrace 5 -nocwarn +--- wise-2.4.1.orig/src/corba/makefile ++++ wise-2.4.1/src/corba/makefile +@@ -3,9 +3,9 @@ + CC = cc + INCFLAGS = -I../base/ -I../dynlibsrc + #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-#CFLAGS = -O2 -c -DUNIX -I../base/ `glib-config --cflags` -I/usr/local/include/orbit-1.0/ +-CFLAGS = -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` +-LFLAGS = -L../base/ -lm -lpthread ++#CFLAGS += -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ ++CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` ++LDFLAGS += -L../base/ -lm -lpthread + AR_OPTIONS = ru + + +@@ -14,18 +14,18 @@ + orbit-idl hspscan_corba.idl + + test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o +- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o +- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `glib-config --libs` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +--- wise-2.4.1.orig/src/models/makefile ++++ wise-2.4.1/src/models/makefile +@@ -62,46 +62,46 @@ + # $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) wise2xhmmer2.c + + testgenestat : testgenestat.o genestats.o pwmdna.o +- $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o testgenestat testgenestat.o genestats.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) + + test_aligng : test_aligng.o aligngenemodel.o pwmdna.o +- $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_aligng test_aligng.o aligngenemodel.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) + + makepwm : makepwm.o pwmdna.o +- $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o makepwm makepwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) + + testwise2xhmmer2.o : testwise2xhmmer2.c + $(CC) $(CFLAGS) -I../HMMer2/ $(INCFLAGS) testwise2xhmmer2.c + + testwise2xhmmer2 : testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o +- $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LFLAGS) ++ $(CC) -o testwise2xhmmer2 wise2xhmmer2.o testwise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o -ldyna -lwisebase -lhmmer $(LDFLAGS) + + plan7test.o : plan7test.c + $(CC) $(CFLAGS) -I../HMMer2/ plan7test.c + + plan7test : plan7test.o plan7.o wise2xhmmer2.o threestatemodel.o threestatedb.o pfamhmmer1db.o +- $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LFLAGS) ++ $(CC) -o plan7test plan7test.o plan7.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o -ldyna -lwisebase -lhmmer $(LDFLAGS) + + seqstat : seqstat.o +- $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o seqstat seqstat.o -ldyna -lwisebase $(LDFLAGS) + + mutatedna : mutatedna.o +- $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o mutatedna mutatedna.o -ldyna -lwisebase $(LDFLAGS) + + revcomp : revcomp.o +- $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o revcomp revcomp.o -ldyna -lwisebase $(LDFLAGS) + + stupid_motif_scan : stupid_motif_scan.o +- $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o stupid_motif_scan stupid_motif_scan.o -ldyna -lwisebase $(LDFLAGS) + + seqtrunc : seqtrunc.o +- $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o seqtrunc seqtrunc.o -ldyna -lwisebase $(LDFLAGS) + + seqlist : seqlist.o +- $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o seqlist seqlist.o -ldyna -lwisebase $(LDFLAGS) + + testpwm : testpwm.o pwmdna.o +- $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LFLAGS) -lefence ++ $(CC) -o testpwm testpwm.o pwmdna.o -ldyna -lwisebase $(LDFLAGS) -lefence + + + threestate : $(MODELOBJ) +@@ -111,29 +111,29 @@ + pwise : $(MODELOBJ) threestatemat.o threestatedisplay.o + + test : test.o proteinsw.o protprotdis.o +- $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LFLAGS) ++ $(CC) -o test test.o proteinsw.o protprotdis.o -ldyna_glib -ldyna -lwisebase ../dynlibsrc/matrix.o $(LDFLAGS) + + testanc : testanc.o proteinsw.o abc.o pba.o sw_wrap.o +- $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o testanc testanc.o proteinsw.o abc.o pba.o sw_wrap.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + test_tf : test_transfactor.o transfactor.o pwmdna.o +- $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_tf test_transfactor.o transfactor.o pwmdna.o $(LDFLAGS) -ldyna -lwisebase + + motifwise : motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o +- $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o motifwise motifwise.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase + + motifcluster : motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o +- $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o motifcluster motifcluster.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase + + motifdiff : motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o +- $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o motifdiff motifdiff.o transfactor.o transregion.o pwmdna.o transregiondp.o $(LDFLAGS) -ldyna -lwisebase + + + cdtest : cdtest.o cdna2genomic.o d2d_display.o +- $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o cdtest cdtest.o cdna2genomic.o d2d_display.o -ldyna_glib -ldyna -lwisebase $(LDFLAGS) + + prob2bits : prob2bits.o +- $(CC) -o prob2bits $(LFLAGS) -ldyna_glib -ldyna -lwisebase ++ $(CC) -o prob2bits $(LDFLAGS) -ldyna_glib -ldyna -lwisebase + + quick : + cc -O -c -I../dynlibsrc/ -I../base/ genewise6.c +@@ -180,161 +180,161 @@ + $(CC) $(CFLAGS) fivestarscan.c -I../base/ -I../dynlibsrc/ -I../HMMer2/ -I. + + oldpostwise : oldpostwise.o $(NEWG) +- $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase ++ $(CC) -g -o oldpostwise oldpostwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase + + testdna : testdna.o dnaalign.o seqaligndisplay.o +- $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o testdna testdna.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + dnal : dnal.o dnaalign.o seqaligndisplay.o +- $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o dnal dnal.o dnaalign.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + psw : psw.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o +- $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + scanwisep.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $? + + hsp2aln_sw.o : hsp2aln_sw.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? + + scanwisep_mysql.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c + + scanwisep_mysql : scanwisep_mysql.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) -lpthread -lZ ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../mysql/protein_index/mysql_protein_index.o $(LDFLAGS) -L../external/mott -L/usr/local/mysql/lib -ldyna_glib -ldyna ott -lwisebase -lmysqlclient -lm $(EXTRALIBS) $(LDFLAGS) -lpthread -lZ + + + scanwisep_corba.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_CORBA -I../corba -I../external/mott `orbit-config --cflags server` scanwisep.c + + scanwisep_corba : scanwisep_corba.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../corba/hspscan_corba-common.o ../corba/hspscan_corba-stubs.o ../corba/corba_singleton.o ../corba/hspscan_corba_wrapper.o $(LDFLAGS) -L../external/mott -ldyna_glib -ldyna -lmott -lwisebase $(EXTRALIBS) `orbit-config --libs server` -lpthread + + + scanwisep_wiseserver.o : scanwisep.c + $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c + + scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread ++ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread + + scanwisep_compress.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c + + scanwisep_compress : scanwisep_compress.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../dnaindex/compressed_protein_index.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o ../dnaindex/kmer_index_interface.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread + + + + scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + test_gwhsp : test_gwhsp.o genewisehsp.o +- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + localcishit.o : localcishit.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? + + promoterwise.o : promoterwise.c +- $(CC) $(CFLAGS) $(INCFLAGS) `glib-config --cflags` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? + + promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o +- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `glib-config --libs` -lpthread ++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread + + dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o +- $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread ++ $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread + + pswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o +- $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + efpswdb : pswdb.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o +- $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS) ++ $(CC) -o pswdb pswdb.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lefence $(EXTRALIBS) + + dba : dbac.o dba.o slimdba.o bigdba.o dbadisplay.o +- $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o dba dbac.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + lba : lba.o largeblockdp.o seqaligndisplay.o +- $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o lba lba.o largeblockdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + fastdba : fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o +- $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o fastdba fastdba.o dba.o slimdba.o bigdba.o dbadisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + evopairwise : evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o +- $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o evopairwise evopairwise.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + test_threestatehsp : test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o threestatehsp.o +- $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o test_threestatehsp test_threestatehsp.o threestatemodel.o threestateloop.o threestatedb.o pfamhmmer1db.o seqaligndisplay.o threestatehsp.o wise2xhmmer2.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + makerandomdb : makerandomdb.o +- $(CC) -o makerandomdb makerandomdb.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + genewise : genewise.o $(NEWG) +- $(CC) -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + cdnawise : cdnawise.o $(NEWG) cdnawise10.o +- $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + fivestar : fivestar.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o fivestar fivestar.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + fivestarsearch : fivestarsearch.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o fivestarsearch fivestarsearch.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + fivestarscan : fivestarscan.o fivestatemodel.o fivestate.o threestatemodel.o threestatedb.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o +- $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o fivestarscan fivestarscan.o fivestatemodel.o fivestate.o threestatedb.o threestatemodel.o pfamhmmer1db.o wise2xhmmer2.o seqaligndisplay.o standardout.o threestatedp.o $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + editdist : editdist.o editdistdp.o standardout.o seqaligndisplay.o +- $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase ++ $(CC) -g -o editdist editdist.o editdistdp.o standardout.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase + + + efgw : genewise.o $(NEWG) +- $(CC) -g -o genewise genewise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence ++ $(CC) -g -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + + + genewisedb : genewisedb.o $(NEWG) +- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + estwisedb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + edb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence ++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + + estwise : estwise.o $(NEWG) +- $(CC) -g -o estwise estwise.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o +- $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o amplimer_resolver amplimer_resolver.o dnamatcher.o dnaalign.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + genomewise : genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneutil.o geneoutput.o +- $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o genomewise genomewise.o genomewise9.o genome_evidence.o est_evidence.o geneoutput.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + sywise : sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o sywise sywise.o sywise20.o syexonmodel.o genestats.o pwmdna.o standardout.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + alignwise : alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o +- $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o alignwise alignwise.o alignwisedp.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o geneoutput.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + test_splice : test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o +- $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o test_splice test_splice.o aligngenemodel.o genestats.o pwmdna.o geneutil.o standardout.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + statwise : statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o +- $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + pseudowise : pseudowise.o pseudowise7.o $(NEWG) +- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o +- $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + + HMMER_LIBS = ../HMMer2/ +@@ -345,11 +345,11 @@ + CC = cc + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS = -c -g3 -O2 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `glib-config --cflags` +-#CFLAGS = -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` +-#LFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ ++CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` ++#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` ++#LDFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ + +-LFLAGS = -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `glib-config --libs` ++LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -360,7 +360,7 @@ + + + #test : test.o libwisedb.a +-# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LFLAGS) ++# $(CC) -o test test.o libwisedb.a -lprob -ldyn -lwisebase $(LDFLAGS) + + + # +--- wise-2.4.1.orig/src/dnaindex/makefile ++++ wise-2.4.1/src/dnaindex/makefile +@@ -27,53 +27,53 @@ + + + kwise : kwise.o $(ASSEMBLY_OBJ) +- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` + + arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) +- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` + + + findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) +- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LFLAGS) `glib-config --libs` ++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` + + make_shotgun : make_shotgun.o shotgun.o +- $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS) + + test_dnanumber : test_dnanumber.o dnanumber.o +- $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_dnanumber test_dnanumber.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) + + test_linkindex : test_linkindex.o linkindex.o dnanumber.o +- $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_linkindex test_linkindex.o linkindex.o dnanumber.o -ldyna -lwisebase $(LDFLAGS) + + test_forwardindex : test_forwardindex.o forwardindex.o +- $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_forwardindex test_forwardindex.o forwardindex.o -ldyna -lwisebase $(LDFLAGS) + + test_euler : test_euler.o eulerindex.o singleseqspace.o +- $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_euler test_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + + test_kmer : test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_contig.o kmer_assembly_error.o assembly.o +- $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_kmer test_kmer.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o kmer_assembly_untangler.o kmer_assembly_error.o kmer_assembly_contig.o assembly.o -ldyna -lwisebase $(LDFLAGS) + + kmer_stat : kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o +- $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o kmer_stat kmer_stat.o kmer_assembly.o kmer_index_interface.o kmer_direct.o singleseqspace.o dnamapping.o largeseqreader.o -ldyna -lwisebase $(LDFLAGS) + + test_compara : test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o +- $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o test_compara test_compara.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) + + bigseqwise : bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o +- $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o bigseqwise bigseqwise.o comparapath.o dnamapping.o singleseqspace.o chhash.o largeseqreader.o kmer_direct.o kmer_hash.o -ldyna -lwisebase $(LDFLAGS) + + + + + show_euler : show_euler.o eulerindex.o singleseqspace.o +- $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LFLAGS) ++ $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + + CC = cc +-CFLAGS = -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` + + +-LFLAGS = -g -L../base/ -L../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm + + + .c.o : +--- wise-2.4.1.orig/src/dnaindex/assembly/makefile ++++ wise-2.4.1/src/dnaindex/assembly/makefile +@@ -3,33 +3,33 @@ + .SUFFIXES : .dy + + test_basegraph : test_basegraph.o basegraph.o +- $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_basegraph test_basegraph.o basegraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o $(LDFLAGS) -ldyna -lwisebase + + test_assemblygraph : test_assemblygraph.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_assemblygraph test_assemblygraph.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + + test_graphtangle : test_graphtangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o +- $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o test_graphtangle test_graphtangle.o assemblystats.o basegraph.o assemblygraph.o graphtangle.o assemblypath.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../kmer_hash.o $(LDFLAGS) -ldyna -lwisebase + + + pathwise : pathwise.o supertangle.o assemblygraph.o assemblystats.o basegraph.o graphtangle.o assemblypath.o grapherror.o graphmanager.o depthmanager.o +- $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o pathwise pathwise.o supertangle.o depthmanager.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o graphtangle.o assemblypath.o grapherror.o graphmanager.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o ../assembly_sanger_project.o $(LDFLAGS) -ldyna -lwisebase + + + badkmer : badkmer.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o badkmer badkmer.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + arraymatcher : arraymatcher.o assemblygraph.o assemblystats.o basegraph.o +- $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LFLAGS) -ldyna -lwisebase ++ $(CC) -o arraymatcher arraymatcher.o assemblystats.o basegraph.o assemblygraph.o ../dnamapping.o ../kmer_index_interface.o ../kmer_glib_index.o ../kmer_hash.o ../assembly.o ../assembly_stream_fasta.o ../largeseqreader.o ../singleseqspace.o ../assembly_stream_interface.o $(LDFLAGS) -ldyna -lwisebase + + + + CC = cc +-CFLAGS = -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0` + + +-LFLAGS = -g -L../../base/ -L../../dynlibsrc/ -lpthread `glib-config --libs` -lm ++LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm + + + .c.o : +--- wise-2.4.1.orig/src/dynlibsrc/makefile ++++ wise-2.4.1/src/dynlibsrc/makefile +@@ -84,11 +84,11 @@ + CC = cc + INCFLAGS = -I../base/ + #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-CFLAGS = -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` +-#CFLAGS = -Wall -g3 -pg -DPTHREAD -O2 -c -DUNIX -I../base/ `glib-config --cflags` +-#CFLAGS = -O2 -c -pthread -DUNIX -I../base/ `glib-config --cflags` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` ++#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` ++#CFLAGS += -c -pthread -DUNIX -I../base/ `pkg-config --cflags glib-2.0` + #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ +-LFLAGS = -g -L../base/ -lm ++LDFLAGS += -g -L../base/ -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -133,47 +133,47 @@ + # + + test_genomic : genomic.o test_genomic.o sequence.o codon.o +- $(CC) -o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS)-o test_genomic test_genomic.o genomic.o sequence.o codon.o ../base/libwisebase.a -lm + + test_tree : tree.o test_tree.o +- $(CC) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o test_tree test_tree.o tree.o libdyna.a ../base/libwisebase.a -lm + + test_intallocator : intallocator.o test_intallocator.o +- $(CC) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o test_intallocator intallocator.o test_intallocator.o ../base/libwisebase.a -lm + + test_psi : test_psi.o proteinstreamedindex.o +- $(CC) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o test_psi test_psi.o proteinstreamedindex.o ./libdyna.a ../base/libwisebase.a -lm + + test_shadowindex : test_shadowindex.o shadowseqindex.o shadowseq.o libdyna.a +- $(CC) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm + + test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a +- $(CC) -g -o test_seqhash `glib-config --libs` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o test_seqhash `pkg-config --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm + + test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` + + test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `glib-config --libs` ++ $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` + + + testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o +- $(CC) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testgendb probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm + + testseqalign : seqalign.o testseqalign.o sequence.o codon.o +- $(CC) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testseqalign testseqalign.o seqalign.o sequence.o codon.o ../base/libwisebase.a -lm + + testanc : libdyna.a +- $(CC) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testanc ../models/testanc.o ../models/proteinsw.o ../models/abc.o ../models/pba.o ../models/sw_wrap.o libdyna.a ../base/libwisebase.a -lm + + testdb : testdb.o sequencedb.o sequence.o codon.o probability.o +- $(CC) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testdb testdb.o sequencedb.o sequence.o codon.o probability.o ../base/libwisebase.a -lm + + testpdb : testpdb.o protein.o proteindb.o complexevalset.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o histogram.o +- $(CC) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -o testpdb testpdb.o protein.o proteindb.o complexsequence.o sequencedb.o sequence.o codon.o probability.o randomdb.o randommodel.o complexevalset.o histogram.o ../base/libwisebase.a -lm + + testpb : testpairbase.o pairbase.o pairbaseseq.o sequence.o seqalign.o codon.o probability.o complexsequence.o complexevalset.o +- $(CC) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o testpb testpairbase.o pairbase.o pairbaseseq.o sequence.o codon.o seqalign.o probability.o complexsequence.o complexevalset.o ../base/libwisebase.a -lm + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +--- wise-2.4.1.orig/src/network/makefile ++++ wise-2.4.1/src/network/makefile +@@ -3,8 +3,8 @@ + + CC = cc + INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex +-CFLAGS = -O2 -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `glib-config --cflags` +-LFLAGS = -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `glib-config --libs` ++CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +@@ -13,7 +13,7 @@ + + + scanwise_server : wise_proteinindex_server.o net_hspscan.o ../dynlibsrc/libdyna.a ../dynlibsrc/libdyna_glib.a ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o +- $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LFLAGS) -lpthread ++ $(CC) -g -o scanwise_server wise_proteinindex_server.o net_hspscan.o ../dnaindex/compressed_protein_index.o ../dnaindex/kmer_index_interface.o ../dnaindex/singleseqspace.o ../dnaindex/kmer_direct.o -ldyna_glib -ldyna -lwisesocket -lwisebase $(LDFLAGS) -lpthread + + + .c.o : +--- wise-2.4.1.orig/src/other_programs/makefile ++++ wise-2.4.1/src/other_programs/makefile +@@ -3,8 +3,8 @@ + .SUFFIXES : .dy + + CC = cc +-CFLAGS = -O2 -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `glib-config --cflags` +-LFLAGS = -g -L../base/ -L../dynlibsrc -lm `glib-config --libs` ++CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `pkg-config --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- wise-2.4.1.orig/src/base/makefile ++++ wise-2.4.1/src/base/makefile +@@ -19,9 +19,9 @@ + + + +-#CFLAGS = -c -g -DUNIX -DWISE_MEMORY_WATCH +-CFLAGS = -c -O2 -DUNIX -pthread +-LFLAGS = -g -lm ++#CFLAGS += -c -g -DUNIX -DWISE_MEMORY_WATCH ++CFLAGS += $(CPPFLAGS) -c -DUNIX -pthread ++LDFLAGS += -g -lm + DFLAGS = -n Wise2_ -a _api.h -b _api.t -l -D + AR_OPTIONS = ru + +--- wise-2.4.1.orig/src/HMMer2/Makefile ++++ wise-2.4.1/src/HMMer2/Makefile +@@ -13,7 +13,7 @@ + ## your compiler and compiler flags + # + CC = cc +-CFLAGS = -g ++CFLAGS += $(CPPFLAGS) -g + + ## machine specific definitions + # +@@ -75,25 +75,25 @@ + all: $(PROGS) + + hmmalign: $(OBJ) hmmalign.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmalign.o $(OBJ) $(LIBS) + + hmmbuild: $(OBJ) hmmbuild.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmbuild.o $(OBJ) $(LIBS) + + hmmcalibrate: $(OBJ) hmmcalibrate.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmcalibrate.o $(OBJ) $(LIBS) + + hmmconvert: $(OBJ) hmmconvert.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmconvert.o $(OBJ) $(LIBS) + + hmmemit: $(OBJ) hmmemit.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmemit.o $(OBJ) $(LIBS) + + hmmpfam: $(OBJ) hmmpfam.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmpfam.o $(OBJ) $(LIBS) + + hmmsearch: $(OBJ) hmmsearch.o +- $(CC) $(CFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) ++ $(CC) $(CFLAGS) $(LDFLAGS) $(MDEFS) -o $@ hmmsearch.o $(OBJ) $(LIBS) + + ####### + ## Target used in making Shiva test suite diff --git a/academic/wise/patches/06_getline.patch b/academic/wise/patches/06_getline.patch new file mode 100644 index 0000000000..341cdae82e --- /dev/null +++ b/academic/wise/patches/06_getline.patch @@ -0,0 +1,305 @@ +Author: Philipp Benner <philipp@debian.org> +Last-Update: Sat, 31 Oct 2009 21:25:52 +0000 +Bug-Debian: http://bugs.debian.org/552821 +Description: Fixed conflicting definitions of getline(). + +--- wise-2.4.1.orig/src/HMMer2/sqio.c ++++ wise-2.4.1/src/HMMer2/sqio.c +@@ -213,7 +213,7 @@ + } + } + +-/* Function: getline() ++/* Function: getline_() + * Date: SRE, Tue Mar 3 08:30:01 1998 [St. Louis] + * + * Purpose: read a line from a sequence file into V->sbuffer. +@@ -229,7 +229,7 @@ + * Returns: (void) + */ + static void +-getline(struct ReadSeqVars *V) ++getline_(struct ReadSeqVars *V) + { + char *cp; + +@@ -299,7 +299,7 @@ + V->seqlen = 0; + if (addfirst) addseq(V->sbuffer, V); + do { +- getline(V); ++ getline_(V); + /* feof() alone is a bug; files not necessarily \n terminated */ + if (*(V->sbuffer) == '\0' && feof(V->f)) + done = TRUE; +@@ -327,7 +327,7 @@ + char *sptr; + /* load first line of entry */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ getline_(V); + if (feof(V->f)) return; + + if ((sptr = strtok(V->sbuffer + 15, "\n\t ")) != NULL) +@@ -336,7 +336,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ID); + } + do { +- getline(V); ++ getline_(V); + if (!feof(V->f) && strncmp(V->sbuffer, "TITLE", 5) == 0) + SetSeqinfoString(V->sqinfo, V->sbuffer+15, SQINFO_DESC); + else if (!feof(V->f) && strncmp(V->sbuffer, "ACCESSION", 9) == 0) +@@ -345,7 +345,7 @@ + SetSeqinfoString(V->sqinfo, sptr, SQINFO_ACC); + } + } while (! feof(V->f) && (strncmp(V->sbuffer,"SEQUENCE", 8) != 0)); +- getline(V); /* skip next line, coords */ ++ getline_(V); /* skip next line, coords */ + + readLoop(0, endPIR, V); + +@@ -359,7 +359,7 @@ + /* get next line + */ + while (!feof(V->f) && strncmp(V->sbuffer, "ENTRY", 5) != 0) +- getline(V); ++ getline_(V); + } + + +@@ -377,7 +377,7 @@ + char *nm; + /* position past ';' comments */ + do { +- getline(V); ++ getline_(V); + } while (! (feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer != ';')) )); + + if (!feof(V->f)) +@@ -389,7 +389,7 @@ + } + + while (!(feof(V->f) || ((*V->sbuffer != '\0') && (*V->sbuffer == ';')))) +- getline(V); ++ getline_(V); + } + + static int +@@ -411,7 +411,7 @@ + if ((nm = strtok(V->sbuffer+16, ",\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, nm, SQINFO_NAME); + } +- getline(V); ++ getline_(V); + } + + if (! feof(V->f)) +@@ -420,7 +420,7 @@ + /* load next line + */ + while ((!feof(V->f)) && (*V->sbuffer != ';')) +- getline(V); ++ getline_(V); + } + + +@@ -438,7 +438,7 @@ + int in_definition; + + while (strncmp(V->sbuffer, "LOCUS", 5) != 0) +- getline(V); ++ getline_(V); + + if ((sptr = strtok(V->sbuffer+12, "\n\t ")) != NULL) + { +@@ -449,7 +449,7 @@ + in_definition = FALSE; + while (! feof(V->f)) + { +- getline(V); ++ getline_(V); + if (! feof(V->f) && strstr(V->sbuffer, "DEFINITION") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+12, "\n")) != NULL) +@@ -482,11 +482,11 @@ + + + while (!(feof(V->f) || ((*V->sbuffer!=0) && (strstr(V->sbuffer,"LOCUS") == V->sbuffer)))) +- getline(V); ++ getline_(V); + /* SRE: V->s now holds "//", so sequential + reads are wedged: fixed Tue Jul 13 1993 */ + while (!feof(V->f) && strstr(V->sbuffer, "LOCUS ") != V->sbuffer) +- getline(V); ++ getline_(V); + } + + static int +@@ -515,7 +515,7 @@ + Die("bogus GCGdata format? %s", V->sbuffer); + + /* second line contains free text description */ +- getline(V); ++ getline_(V); + SetSeqinfoString(V->sqinfo, V->sbuffer, SQINFO_DESC); + + if (binary) { +@@ -535,7 +535,7 @@ + else readLoop(0, endGCGdata, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ getline_(V); + } + + static int +@@ -555,12 +555,12 @@ + if ((sptr = strtok(NULL, "\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_DESC); + /* workaround for long NCBI NR lines */ +- while (V->longline && ! feof(V->f)) getline(V); ++ while (V->longline && ! feof(V->f)) getline_(V); + + readLoop(0, endPearson, V); + + while (!(feof(V->f) || ((*V->sbuffer != 0) && (*V->sbuffer == '>')))) +- getline(V); ++ getline_(V); + } + + +@@ -587,7 +587,7 @@ + + /* make sure we have first line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ getline_(V); + + if ((sptr = strtok(V->sbuffer+5, "\n\t ")) != NULL) + { +@@ -596,7 +596,7 @@ + } + + do { +- getline(V); ++ getline_(V); + if (!feof(V->f) && strstr(V->sbuffer, "AC ") == V->sbuffer) + { + if ((sptr = strtok(V->sbuffer+5, "; \t\n")) != NULL) +@@ -620,7 +620,7 @@ + + /* load next record's ID line */ + while (!feof(V->f) && strncmp(V->sbuffer, "ID ", 4) != 0) +- getline(V); ++ getline_(V); + } + + +@@ -636,7 +636,7 @@ + { + char *sptr; + +- getline(V); /*s == "seqLen seqid string..."*/ ++ getline_(V); /*s == "seqLen seqid string..."*/ + + if ((sptr = strtok(V->sbuffer+6, " \t\n")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -647,7 +647,7 @@ + readLoop(0, endZuker, V); + + while (!(feof(V->f) | ((*V->sbuffer != '\0') & (*V->sbuffer == '(')))) +- getline(V); ++ getline_(V); + } + + static void +@@ -669,7 +669,7 @@ + + do { + done = feof(V->f); +- getline(V); ++ getline_(V); + if (! done) addseq(V->sbuffer, V); + } while (!done); + } +@@ -681,7 +681,7 @@ + char *sptr; + int dostruc = FALSE; + +- while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline(V); ++ while (strncmp(V->sbuffer, "NAM ", 4) != 0) getline_(V); + + if ((sptr = strtok(V->sbuffer+4, "\n\t ")) != NULL) + SetSeqinfoString(V->sqinfo, sptr, SQINFO_NAME); +@@ -689,7 +689,7 @@ + /*CONSTCOND*/ + while (1) + { +- getline(V); ++ getline_(V); + if (feof(V->f)) {squid_errno = SQERR_FORMAT; return; } + + if (strncmp(V->sbuffer, "SRC ", 4) == 0) +@@ -721,14 +721,14 @@ + while (1) + { + /* sequence line */ +- getline(V); ++ getline_(V); + if (feof(V->f) || strncmp(V->sbuffer, "++", 2) == 0) + break; + addseq(V->sbuffer, V); + /* structure line */ + if (dostruc) + { +- getline(V); ++ getline_(V); + if (feof(V->f)) { squid_errno = SQERR_FORMAT; return; } + addstruc(V->sbuffer, V); + } +@@ -736,7 +736,7 @@ + + + while (!feof(V->f) && strncmp(V->sbuffer, "NAM ", 4) != 0) +- getline(V); ++ getline_(V); + } + + +@@ -816,7 +816,7 @@ + + /* Load the first line. + */ +- getline(dbfp); ++ getline_(dbfp); + + return dbfp; + } +@@ -833,7 +833,7 @@ + Die("SeqfilePosition() failed: in a nonrewindable data file or stream"); + + fseek(sqfp->f, offset, SEEK_SET); +- getline(sqfp); ++ getline_(sqfp); + } + + +@@ -853,7 +853,7 @@ + if (sqfp->ali_aseqs != NULL) sqfp->ali_curridx = 0; + else { + rewind(sqfp->f); +- getline(sqfp); ++ getline_(sqfp); + } + } + +@@ -949,7 +949,7 @@ + do { /* skip leading comments on GCG file */ + gotuw = (strstr(V->sbuffer,"..") != NULL); + if (gotuw) readUWGCG(V); +- getline(V); ++ getline_(V); + } while (! feof(V->f)); + break; + diff --git a/academic/wise/patches/07_ld--as-needed.patch b/academic/wise/patches/07_ld--as-needed.patch new file mode 100644 index 0000000000..51ee254370 --- /dev/null +++ b/academic/wise/patches/07_ld--as-needed.patch @@ -0,0 +1,52 @@ +Description: Fix FTBFS with ld --as-needed. +Bug-Ubuntu: https://bugs.launchpad.net/ubuntu/+source/wise/+bug/832935 + +--- wise-2.4.1.orig/src/models/makefile ++++ wise-2.4.1/src/models/makefile +@@ -215,7 +215,7 @@ + $(CC) $(CFLAGS) $(INCFLAGS) -o scanwisep_wiseserver.o -DSCAN_WISESERVER -I../network -I../socket -I../external/mott scanwisep.c + + scanwise : scanwisep_wiseserver.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread ++ $(CC) -o scanwise scanwisep_wiseserver.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o ../network/net_hspscan.o ../network/client_multihspscan.o $(LDFLAGS) -L../external/mott -L../socket -lmott -ldyna_glib -ldyna -lwisesocket -lwisebase $(EXTRALIBS) -lpthread $(LDFLAGS) + + scanwisep_compress.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_COMPRESS -I../dnaindex -I../network -I../socket -I../external/mott scanwisep.c +@@ -275,7 +275,7 @@ + $(CC) -o makerandomdb makerandomdb.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + genewise : genewise.o $(NEWG) +- $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -o genewise genewise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + cdnawise : cdnawise.o $(NEWG) cdnawise10.o + $(CC) -g -o cdnawise cdnawise.o cdnawise10.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) +@@ -300,16 +300,16 @@ + + + genewisedb : genewisedb.o $(NEWG) +- $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o genewisedb genewisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + estwisedb : estwisedb.o $(NEWG) +- $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + edb : estwisedb.o $(NEWG) + $(CC) -g -o estwisedb estwisedb.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) -lefence + + estwise : estwise.o $(NEWG) +- $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o estwise estwise.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + + amplimer_resolver : amplimer_resolver.o dnaalign.o dnamatcher.o +@@ -331,7 +331,7 @@ + $(CC) -g -o statwise statwise.o statwise10.o syexonmodel.o genestats.o pwmdna.o geneutil.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + pseudowise : pseudowise.o pseudowise7.o $(NEWG) +- $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) ++ $(CC) -g -o pseudowise pseudowise.o pseudowise7.o $(NEWG) $(LDFLAGS) -lhmmer -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) $(LDFLAGS) + + clonewise : clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o + $(CC) -g -o clonewise clonewise.o clonewisedp.o localclonewisedp.o mapstruct.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) diff --git a/academic/wise/patches/08_mayhem.patch b/academic/wise/patches/08_mayhem.patch new file mode 100644 index 0000000000..c54c7c66ab --- /dev/null +++ b/academic/wise/patches/08_mayhem.patch @@ -0,0 +1,103 @@ +Author: Philipp Benner <philipp@debian.org> +Last-Update: Sun, 07 Jul 2013 13:33:01 +0200 +Description: Fix run time errors detected by Mayhem + +--- wise-2.4.1.orig/src/models/dbac.c ++++ wise-2.4.1/src/models/dbac.c +@@ -535,8 +535,12 @@ + * + */ + +- one = read_fasta_file_Sequence(*argv++); +- two = read_fasta_file_Sequence(*argv++); ++ if( (one = read_fasta_file_Sequence(*argv++)) == NULL ) { ++ fatal("Unable to read the sequence in file"); ++ } ++ if( (two = read_fasta_file_Sequence(*argv++)) == NULL ) { ++ fatal("Unable to read the sequence in file"); ++ } + + uppercase_Sequence(one); + uppercase_Sequence(two); +--- wise-2.4.1.orig/src/models/estwise.c ++++ wise-2.4.1/src/models/estwise.c +@@ -313,7 +313,7 @@ + } + } + +- if( reverse == TRUE ) { ++ if( cdna && reverse == TRUE ) { + if( tstart > tend ) { + warn("You have already reversed the DNA by using %d - %d truncation. Re-reversing",tstart,tend); + } +@@ -323,7 +323,7 @@ + cdna = cdna_temp; + } + +- if( target_abs == TRUE ) { ++ if( cdna && target_abs == TRUE ) { + cdna->baseseq->offset = 1; + cdna->baseseq->end = strlen(cdna->baseseq->seq); + } +@@ -472,8 +472,11 @@ + } + + cp = flat_cDNAParser(indel_error); +- cm = flat_CodonMapper(ct); +- sprinkle_errors_over_CodonMapper(cm,subs_error); ++ ++ if( ct ) { ++ cm = flat_CodonMapper(ct); ++ sprinkle_errors_over_CodonMapper(cm,subs_error); ++ } + + return ret; + +--- wise-2.4.1.orig/src/models/genewise.c ++++ wise-2.4.1/src/models/genewise.c +@@ -550,8 +550,10 @@ + ret = FALSE; + } + +- gen->baseseq->offset = 1; +- gen->baseseq->end = strlen(gen->baseseq->seq); ++ if ( gen ) { ++ gen->baseseq->offset = 1; ++ gen->baseseq->end = strlen(gen->baseseq->seq); ++ } + } + + if( alg_str != NULL ) { +--- wise-2.4.1.orig/src/models/estwisedb.c ++++ wise-2.4.1/src/models/estwisedb.c +@@ -688,8 +688,11 @@ + + + cps = flat_cDNAParser(indel_error); +- cm = flat_CodonMapper(ct); +- sprinkle_errors_over_CodonMapper(cm,subs_error); ++ ++ if( ct ) { ++ cm = flat_CodonMapper(ct); ++ sprinkle_errors_over_CodonMapper(cm,subs_error); ++ } + + return ret; + +--- wise-2.4.1.orig/src/models/promoterwise.c ++++ wise-2.4.1/src/models/promoterwise.c +@@ -147,8 +147,12 @@ + + lchs = standard_LocalCisHitScore(NMaskType_VARIABLE); + +- query = read_fasta_file_Sequence(argv[1]); +- target = read_fasta_file_Sequence(argv[2]); ++ if( (query = read_fasta_file_Sequence(argv[1])) == NULL ) { ++ fatal("Unable to read the sequence in query file"); ++ } ++ if( (target = read_fasta_file_Sequence(argv[2])) == NULL ) { ++ fatal("Unable to read the sequence in target file"); ++ } + + for(i=0;i<query->len;i++) { + query->seq[i] = toupper(query->seq[i]); diff --git a/academic/wise/patches/09_dnal-add-return-statement.patch b/academic/wise/patches/09_dnal-add-return-statement.patch new file mode 100644 index 0000000000..62931ed624 --- /dev/null +++ b/academic/wise/patches/09_dnal-add-return-statement.patch @@ -0,0 +1,17 @@ +Author: Dejan Latinovic <Dejan.Latinovic@imgtec.com> +Last-Update: Mon, 4 Aug 2014 17:10:38 +0000 +Bug-Debian: http://bugs.debian.org/751277 +Description: Make sure dnal has a valid return value + This affects a bug reported against python-biopython. + +--- wise-2.4.1.orig/src/models/dnal.c ++++ wise-2.4.1/src/models/dnal.c +@@ -75,6 +75,8 @@ + + if( show_alb == TRUE ) + dump_ascii_AlnBlock(alb,stdout); ++ ++ return 0; + } + + diff --git a/academic/wise/patches/10_fix_path_to_data_files.patch b/academic/wise/patches/10_fix_path_to_data_files.patch new file mode 100644 index 0000000000..f437241cd1 --- /dev/null +++ b/academic/wise/patches/10_fix_path_to_data_files.patch @@ -0,0 +1,337 @@ +Author: Andreas Tille <tille@debian.org> +Last-Update: Mon, 04 Aug 2014 19:25:58 +0200 +Description: Brute force patch to fix the PATH to the data files to make the + tools finding the needed data for the test suite + . + In principle the PATH should be configurable and the test suite script even + contains a parameter (-cf) for this - but this seems to be ignored. + . + The correct way to deal with this would be a configuration option but I had + no intend to spend to much time into some software that was declared to be + orphaned (superseded by exonerate). So this primitive patch works to run + the test suite successfully (which is not the case without the patch). + +--- a/src/models/estwise.c ++++ b/src/models/estwise.c +@@ -484,8 +484,8 @@ boolean build_objects(void) + + void build_defaults(void) + { +- codon_file = "codon.table"; +- matrix_file = "BLOSUM62.bla"; ++ codon_file = "/usr/share/wise/codon.table"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + + +--- a/src/models/estwisedb.c ++++ b/src/models/estwisedb.c +@@ -78,7 +78,7 @@ char * qend_str = NULL; + int qend = -1; + + +-char * matrix_file = "BLOSUM62.bla"; ++char * matrix_file = "/usr/share/wise/BLOSUM62.bla"; + CompMat * mat = NULL; + + char * gap_str = "12"; +@@ -849,8 +849,8 @@ void show_version(FILE * ofp) + + void build_defaults(void) + { +- codon_file = "codon.table"; +- matrix_file = "BLOSUM62.bla"; ++ codon_file = "/usr/share/wise/codon.table"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + + } +--- a/src/models/pswdb.c ++++ b/src/models/pswdb.c +@@ -40,7 +40,7 @@ int max_desc = 500; + + char * querydb = NULL; + char * targetdb = NULL; +-char * matrix_file = "BLOSUM62.bla"; ++char * matrix_file = "/usr/share/wise/BLOSUM62.bla"; + char * output_file = "-"; + + char * cutoff_str = NULL; +@@ -65,7 +65,7 @@ void show_help(FILE * ofp) + fprintf(ofp,"\npswdb <options> <query_db> <target_db>\nSeqs in fasta format\n" + "\t-g gap penalty (default 12)\n" + "\t-e ext penatly (default 2)\n" +- "\t-m comp matrix (default BLOSUM62.bla)\n" ++ "\t-m comp matrix (default /usr/share/wise/BLOSUM62.bla)\n" + "\t-abc use the abc model\n" + "\t-a a penalty for above (default 120)\n" + "\t-b b penalty for above (default 10)\n" +@@ -397,7 +397,7 @@ int main(int argc,char *argv[]) + + matrix_file = strip_out_assigned_argument(&argc,argv,"m"); + if( matrix_file == NULL) +- matrix_file = "BLOSUM62.bla"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + /* database implementation stuff */ + dbsi = new_DBSearchImpl_from_argv(&argc,argv); +--- a/src/models/genewisedb.c ++++ b/src/models/genewisedb.c +@@ -77,7 +77,7 @@ int qend = -1; + char * gene_file = NULL; + GeneFrequency21 * gf = NULL; + +-char * matrix_file = "BLOSUM62.bla"; ++char * matrix_file = "/usr/share/wise/BLOSUM62.bla"; + CompMat * mat = NULL; + + char * gap_str = "12"; +@@ -1015,9 +1015,9 @@ void show_version(FILE * ofp) + + void build_defaults(void) + { +- gene_file = "human.gf"; +- codon_file = "codon.table"; +- matrix_file = "BLOSUM62.bla"; ++ gene_file = "/usr/share/wise/human.gf"; ++ codon_file = "/usr/share/wise/codon.table"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + + } +--- a/src/models/genewise.c ++++ b/src/models/genewise.c +@@ -749,10 +749,10 @@ boolean build_objects(void) + + void build_defaults(void) + { +- gene_file = "human.gf"; +- new_gene_file = "gene.stat"; +- codon_file = "codon.table"; +- matrix_file = "BLOSUM62.bla"; ++ gene_file = "/usr/share/wise/human.gf"; ++ new_gene_file = "/usr/share/wise/gene.stat"; ++ codon_file = "/usr/share/wise/codon.table"; ++ matrix_file = "/usr/share/wise/BLOSUM62.bla"; + + + } +--- a/src/models/scanwisep.c ++++ b/src/models/scanwisep.c +@@ -157,7 +157,7 @@ ScanWiseHSPImpl * new_ScanWiseHSPImpl_fr + out->use_multiscan = FALSE; + out->ior_file = NULL; + out->direct_sequence = NULL; +- out->matrix_file = "BLOSUM62.bla"; ++ out->matrix_file = "/usr/share/wise/BLOSUM62.bla"; + out->step = 32; + out->host = "localhost"; + out->port = 4050; +@@ -546,7 +546,7 @@ int main(int argc,char ** argv) + + /* ugly, but we don't want to bounce matrices around the network... */ + +- mat = read_Blast_file_CompMat("BLOSUM62.bla"); ++ mat = read_Blast_file_CompMat("/usr/share/wise/BLOSUM62.bla"); + + erroroff(REPORT); + +--- a/src/models/psw.c ++++ b/src/models/psw.c +@@ -24,7 +24,7 @@ void show_help(FILE * ofp) + "\tOPTIONS\n" + "\t-g gap penalty (default 12)\n" + "\t-e ext penatly (default 2)\n" +- "\t-m comp matrix (default BLOSUM62.bla)\n" ++ "\t-m comp matrix (default /usr/share/wise/BLOSUM62.bla)\n" + "\t-abc use the abc model\n" + "\t-a a penalty for above (default 120)\n" + "\t-b b penalty for above (default 10)\n" +@@ -126,7 +126,7 @@ int main(int argc,char ** argv) + + comp_file = strip_out_assigned_argument(&argc,argv,"m"); + if( comp_file == NULL) +- comp_file = "BLOSUM62.bla"; ++ comp_file = "/usr/share/wise/BLOSUM62.bla"; + + if( (temp = strip_out_assigned_argument(&argc,argv,"dpenv")) != NULL ) { + dpenv = read_DPEnvelope_file(temp); +--- a/src/test/basic_cdna.out ++++ b/src/test/basic_cdna.out +@@ -3,13 +3,13 @@ This program is freely distributed under + Copyright (c) GRL limited: portions of the code are from separate copyrights + + Query protein: roa1_drome +-Comp Matrix: BLOSUM62.bla ++Comp Matrix: /usr/share/wise/BLOSUM62.bla + Gap open: 12 + Gap extension: 2 + Start/End default + Target Sequence HSHNCPA1 + Strand: both +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Algorithm 333 +--- a/src/test/basic_genomic.out ++++ b/src/test/basic_genomic.out +@@ -3,17 +3,17 @@ This program is freely distributed under + Copyright (c) GRL limited: portions of the code are from separate copyright + + Query protein: roa1_drome +-Comp Matrix: BLOSUM62.bla ++Comp Matrix: /usr/share/wise/BLOSUM62.bla + Gap open: 12 + Gap extension: 2 + Start/End default + Target Sequence HSHNCPA1 + Strand: forward + Start/End (protein) default +-Gene Parameter file: gene.stat ++Gene Parameter file: /usr/share/wise/gene.stat + Splice site model: GT/AG only + GT/AG bits penalty -9.96 +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-06 + Indel error: 1e-06 + Null model syn +--- a/src/test/pswdb.out ++++ b/src/test/pswdb.out +@@ -12,7 +12,7 @@ Gap open: 12 + Gap extension: 2 + Query info from: road.pep + Database info from: pep.fa +-Comp Matrix: BLOSUM62.bla ++Comp Matrix: /usr/share/wise/BLOSUM62.bla + [Warning: Can't fit histogram to a db smaller than 1,000] + + +--- a/src/models/genestats.c ++++ b/src/models/genestats.c +@@ -22,7 +22,7 @@ void show_help_GeneModelParam(FILE * ofp + fprintf(ofp," -splice_score_offset [%.1f] score offset for splice sites\n",DEFAULT_SPLICE_OFFSET_SCORE); + fprintf(ofp," -[no]splice_gtag make just gtag splice sites (default is gtag, ie no model)\n"); + fprintf(ofp," -splice_gtag_prob [0.001] probability for gt/ag \n"); +- fprintf(ofp," -genestats [gene.stat]\n"); ++ fprintf(ofp," -genestats [/usr/share/wise/gene.stat]\n"); + + } + +@@ -270,7 +270,7 @@ GeneModelParam * std_GeneModelParam(void + out->min_collar = -5.0; + out->max_collar = +5.0; + out->score_offset = DEFAULT_SPLICE_OFFSET_SCORE; +- out->gene_stats_file = stringalloc("gene.stat"); ++ out->gene_stats_file = stringalloc("/usr/share/wise/gene.stat"); + out->use_gtag_splice = TRUE; + + out->prob_for_gtag = 0.001; +--- a/src/models/genestats.dy ++++ b/src/models/genestats.dy +@@ -103,7 +103,7 @@ void show_help_GeneModelParam(FILE * ofp + fprintf(ofp," -splice_score_offset [%.1f] score offset for splice sites\n",DEFAULT_SPLICE_OFFSET_SCORE); + fprintf(ofp," -[no]splice_gtag make just gtag splice sites (default is gtag, ie no model)\n"); + fprintf(ofp," -splice_gtag_prob [0.001] probability for gt/ag \n"); +- fprintf(ofp," -genestats [gene.stat]\n"); ++ fprintf(ofp," -genestats [/usr/share/wise/gene.stat]\n"); + + } + +@@ -290,7 +290,7 @@ GeneModelParam * std_GeneModelParam(void + out->min_collar = -5.0; + out->max_collar = +5.0; + out->score_offset = DEFAULT_SPLICE_OFFSET_SCORE; +- out->gene_stats_file = stringalloc("gene.stat"); ++ out->gene_stats_file = stringalloc("/usr/share/wise/gene.stat"); + out->use_gtag_splice = TRUE; + + out->prob_for_gtag = 0.001; +--- a/src/models/testgenestat.c ++++ b/src/models/testgenestat.c +@@ -23,7 +23,7 @@ int main(int argc,char ** argv) + + seq = read_fasta_file_Sequence("../../test_data/human.genomic"); + +- ifp = openfile("gene.stat","r"); ++ ifp = openfile("/usr/share/wise/gene.stat","r"); + + st = read_GeneStats(ifp); + +--- a/src/test/hmm_genomic.out ++++ b/src/test/hmm_genomic.out +@@ -7,10 +7,10 @@ Start/End local + Target Sequence HSHNCPA1 + Strand: forward + Start/End (protein) local +-Gene Parameter file: gene.stat ++Gene Parameter file: /usr/share/wise/gene.stat + Splice site model: GT/AG only + GT/AG bits penalty -9.96 +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-06 + Indel error: 1e-06 + Null model syn +--- a/src/test/hmm_cdna.out ++++ b/src/test/hmm_cdna.out +@@ -6,7 +6,7 @@ Query model: unnamed + Start/End default + Target Sequence HSHNCPA1 + Strand: both +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Algorithm 333L +--- a/src/test/genewise-db.out ++++ b/src/test/genewise-db.out +@@ -12,8 +12,8 @@ Search mode: Single protein vs + Protein info from: rrm.HMM + Dna info from: dna.db + Start/End (protein) global +-Gene Paras: human.gf +-Codon Table: codon.table ++Gene Paras: /usr/share/wise/human.gf ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Model splice? model +--- a/src/test/genewise-db-lite.out ++++ b/src/test/genewise-db-lite.out +@@ -12,8 +12,8 @@ Search mode: Single protein vs + Protein info from: rrm.HMM + Dna info from: dna.db + Start/End (protein) global +-Gene Paras: human.gf +-Codon Table: codon.table ++Gene Paras: /usr/share/wise/human.gf ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Model splice? model +--- a/src/test/estwise-db.out ++++ b/src/test/estwise-db.out +@@ -13,7 +13,7 @@ Search mode: Single protein vs + Protein info from: rrm.HMM + Dna info from: dna.db + Start/End local +-Codon Table: codon.table ++Codon Table: /usr/share/wise/codon.table + Subs error: 0.01 + Indel error: 0.01 + Null model: synchronous +--- a/src/test/genewisedb-pfam.out ++++ b/src/test/genewisedb-pfam.out +@@ -12,8 +12,8 @@ Search mode: Single genomic vs + Protein info from: rrm.HMM + Dna info from: short.dna + Start/End (protein) default +-Gene Paras: human.gf +-Codon Table: codon.table ++Gene Paras: /usr/share/wise/human.gf ++Codon Table: /usr/share/wise/codon.table + Subs error: 1e-05 + Indel error: 1e-05 + Model splice? model diff --git a/academic/wise/patches/11_consistent_manual_dates.patch b/academic/wise/patches/11_consistent_manual_dates.patch new file mode 100644 index 0000000000..eaea1eec90 --- /dev/null +++ b/academic/wise/patches/11_consistent_manual_dates.patch @@ -0,0 +1,53 @@ +Description: Use fixed dates for manuals. + These make the build reproducible. I have picked the file modificatin dates of + the corresponding source .tex files. +Author: Sascha Steinbiss <sascha@steinbiss.name> +--- a/docs/dynamite.tex ++++ b/docs/dynamite.tex +@@ -1,4 +1,5 @@ + \documentstyle{article} ++\pdftrailerid{} + \begin{document} + + \newcommand{\programtext}[1]{{\tt #1}} +@@ -10,6 +11,7 @@ + Hinxton, Cambridge CB10 1SA,\\ + England.\\ + Email: birney@sanger.ac.uk} ++\date{18/6/2001} + + \maketitle + +--- a/docs/wise2.tex ++++ b/docs/wise2.tex +@@ -1,5 +1,6 @@ + + \documentclass{article} ++\pdftrailerid{} + %\usepackage{epsfig} + \usepackage{graphicx} + +@@ -13,6 +14,7 @@ + Hinxton, Cambridge CB10 1SD,\\ + England.\\ + Email: birney@ebi.ac.uk} ++\date{18/6/2001} + + \maketitle + +--- a/docs/wise2api.tex ++++ b/docs/wise2api.tex +@@ -1,4 +1,5 @@ + \documentstyle{article} ++\pdftrailerid{} + \begin{document} + + \newcommand{\programtext}[1]{{\tt #1}} +@@ -10,6 +11,7 @@ + Hinxton, Cambridge CB10 1SA,\\ + England.\\ + Email: birney@sanger.ac.uk} ++\date{18/6/2001} + + \maketitle + diff --git a/academic/wise/patches/cross.patch b/academic/wise/patches/cross.patch new file mode 100644 index 0000000000..f6da1363d0 --- /dev/null +++ b/academic/wise/patches/cross.patch @@ -0,0 +1,266 @@ +Date: Sat, 18 Apr 2020 11:59:09 +0200 +From: Helmut Grohne <helmut@subdivi.de> +Bug-Debian: https://bugs.debian.org/958094 +Description: Do not hard code the build architecture pkg-config + +--- a/src/corba/makefile ++++ b/src/corba/makefile +@@ -1,9 +1,10 @@ + + + CC = cc ++PKG_CONFIG ?= pkg-config + INCFLAGS = -I../base/ -I../dynlibsrc + #gCFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-#CFLAGS += -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ ++#CFLAGS += -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` -I/usr/local/include/orbit-1.0/ + CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client` + LDFLAGS += -L../base/ -lm -lpthread + AR_OPTIONS = ru +@@ -14,18 +15,18 @@ hspscan_corba.c : hspscan_corba.idl + orbit-idl hspscan_corba.idl + + test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_server test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna.a ../base/libwisebase.a ../dynlibsrc/hsp.o ../dynlibsrc/subseqhash.o ../dynlibsrc/linkedlist_lookpos.o ../dynlibsrc/libdyna_glib.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + scanwise_protein_index : scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o +- cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -o scanwise_protein_index scanwise_protein_index.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o ../dynlibsrc/libdyna_glib.a ../dynlibsrc/libdyna.a ../base/libwisebase.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_client : test_client.o hspscan_corba-common.o hspscan_corba-stubs.o +- cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_client test_client.o hspscan_corba-common.o hspscan_corba-stubs.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + + test_wrapper : test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o hspscan_corba_wrapper.o corba_singleton.o +- cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `pkg-config --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread ++ cc -g -o test_wrapper test_wrapper.o hspscan_corba-common.o hspscan_corba-stubs.o corba_singleton.o hspscan_corba_wrapper.o ../dynlibsrc/hsp.o ../dynlibsrc/libdyna.a ../base/libwisebase.a `$(PKG_CONFIG) --libs glib-2.0` -lm -lORBit -lIIOP -lORBitutil -lpthread + + .c.o : + $(CC) $(CFLAGS) $(INCFLAGS) $? +--- a/src/dnaindex/assembly/makefile ++++ b/src/dnaindex/assembly/makefile +@@ -26,10 +26,11 @@ arraymatcher : arraymatcher.o assemblygr + + + CC = cc +-CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `pkg-config --cflags glib-2.0` ++PKG_CONFIG ?= pkg-config ++CFLAGS += $(CPPFLAGS) -Wall -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../../base/ -I../../dynlibsrc/ -I../ -I../../models/ `$(PKG_CONFIG) --cflags glib-2.0` + + +-LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm ++LDFLAGS += -g -L../../base/ -L../../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lm + + + .c.o : +--- a/src/dnaindex/makefile ++++ b/src/dnaindex/makefile +@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ) + + + kwise : kwise.o $(ASSEMBLY_OBJ) +- $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` ++ $(CC) -o kwise kwise.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0` + + arraymatcher : arraymatcher.o $(ASSEMBLY_OBJ) +- $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` ++ $(CC) -o arraymatcher arraymatcher.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0` + + + findbad_kmer : findbad_kmer.o $(ASSEMBLY_OBJ) +- $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `pkg-config --libs glib-2.0` ++ $(CC) -o findbad_kmer findbad_kmer.o $(ASSEMBLY_OBJ) -ldyna -lwisebase $(LDFLAGS) `$(PKG_CONFIG) --libs glib-2.0` + + make_shotgun : make_shotgun.o shotgun.o + $(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS) +@@ -70,10 +70,11 @@ show_euler : show_euler.o eulerindex.o s + $(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS) + + CC = cc +-CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` ++PKG_CONFIG ?= pkg-config ++CFLAGS += $(CPPFLAGS) -pthread -c -DHAS_PTHREAD_SETSCOPE -g -DUNIX -I../base/ -I../dynlibsrc/ `$(PKG_CONFIG) --cflags glib-2.0` + + +-LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lm + + + .c.o : +--- a/src/dynlibsrc/makefile ++++ b/src/dynlibsrc/makefile +@@ -82,11 +82,12 @@ DYNHELPEROBJ = packaln.o \ + + + CC = cc ++PKG_CONFIG ?= pkg-config + INCFLAGS = -I../base/ + #CFLAGS = -Wall -g -pedantic -c -DUNIX -I../base/ +-CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` +-#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `pkg-config --cflags glib-2.0` +-#CFLAGS += -c -pthread -DUNIX -I../base/ `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -Wall -pthread -g3 -DCOMPILE_VERBOSITY -DPTHREAD -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` ++#CFLAGS += -Wall -g3 -pg -DPTHREAD -c -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` ++#CFLAGS += -c -pthread -DUNIX -I../base/ `$(PKG_CONFIG) --cflags glib-2.0` + #CFLAGS = -O -c -DUNIX -DNOERROR -I../base/ + LDFLAGS += -g -L../base/ -lm + AR_OPTIONS = ru +@@ -148,13 +149,13 @@ test_shadowindex : test_shadowindex.o sh + $(CC) $(LDFLAGS) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm + + test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a +- $(CC) $(LDFLAGS) -g -o test_seqhash `pkg-config --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm ++ $(CC) $(LDFLAGS) -g -o test_seqhash `$(PKG_CONFIG) --libs glib-2.0` test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a ../base/libwisebase.a -lm + + test_hsp : test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` ++ $(CC) $(LDFLAGS) -g -o test_hsp test_hsp.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `$(PKG_CONFIG) --libs glib-2.0` + + test_topscore : test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o +- $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `pkg-config --libs glib-2.0` ++ $(CC) $(LDFLAGS) -g -o test_topscore test_topscore.o codon.o sequence.o hsp.o compmat.o probability.o ../base/libwisebase.a -lm `$(PKG_CONFIG) --libs glib-2.0` + + + testgendb : probability.o genomicdb.o genomic.o testgendb.o sequence.o codon.o sequencedb.o complexsequence.o complexevalset.o +--- a/src/makefile ++++ b/src/makefile +@@ -23,6 +23,7 @@ + # Most likely you have a non ANSI C compiler + # CC = /opt/intel_cc_80/bin/icc + CC = cc ++PKG_CONFIG ?= pkg-config + + # These are the CFLAGS to use. These days Wise2 is inherently + # pthreaded, and everything is compiled with threads. However +@@ -31,13 +32,13 @@ CC = cc + + + # Intel icc flags +-# CFLAGS += -c -axWK -ipo `pkg-config --cflags glib-2.0` ++# CFLAGS += -c -axWK -ipo `$(PKG_CONFIG) --cflags glib-2.0` + + # alpha flags (-pthread) +-# CFLAGS += -c -pthread `pkg-config --cflags glib-2.0` ++# CFLAGS += -c -pthread `$(PKG_CONFIG) --cflags glib-2.0` + + # normal linux/bsd/mac flags +-CFLAGS += $(CPPFLAGS) -c `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -c `$(PKG_CONFIG) --cflags glib-2.0` + + + EXTRALIBS = -lm +--- a/src/models/makefile ++++ b/src/models/makefile +@@ -192,10 +192,10 @@ psw : psw.o seqaligndisplay.o proteinsw. + $(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) + + scanwisep.o : scanwisep.c +- $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `pkg-config --cflags glib-2.0` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) -I../external/mott `$(PKG_CONFIG) --cflags glib-2.0` $? + + hsp2aln_sw.o : hsp2aln_sw.c +- $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $? + + scanwisep_mysql.o : scanwisep.c + $(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c +@@ -226,25 +226,25 @@ scanwisep_compress : scanwisep_compress. + + + scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o +- $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -o scanwisep scanwisep.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o hsp2aln_sw.o $(LDFLAGS) -L../external/mott -lmott -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + test_gwhsp : test_gwhsp.o genewisehsp.o +- $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -o test_gwhsp test_gwhsp.o genewisehsp.o $(LDFLAGS) -ldyna_glib -ldyna_glib -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + localcishit.o : localcishit.c +- $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $? + + promoterwise.o : promoterwise.c +- $(CC) $(CFLAGS) $(INCFLAGS) `pkg-config --cflags glib-2.0` $? ++ $(CC) $(CFLAGS) $(INCFLAGS) `$(PKG_CONFIG) --cflags glib-2.0` $? + + promoterwise : promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o +- $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -g -o promoterwise promoterwise.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + test_deng : test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -o test_deng test_deng.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + promotercluster : promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o +- $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `pkg-config --libs glib-2.0` -lpthread ++ $(CC) -o promotercluster promotercluster.o localdba.o localcishit.o localcispara.o dbadisplay.o motifmatrix.o motifmatrixdp.o transfactor.o pwmdna.o pairwiseshortdna.o dnaprofile.o dnaprofiledp.o dnaprofileengine.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS) `$(PKG_CONFIG) --libs glib-2.0` -lpthread + + dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o + $(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread +@@ -343,13 +343,14 @@ HMMER_DEFINE = + + + CC = cc ++PKG_CONFIG ?= pkg-config + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` +-#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `pkg-config --cflags glib-2.0` ++CFLAGS += -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `$(PKG_CONFIG) --cflags glib-2.0` ++#CFLAGS += -c -g -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ `$(PKG_CONFIG) --cflags glib-2.0` + #LDFLAGS = -L../base/ -L../dynlibsrc/ -L../HMMer2/ + +-LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `pkg-config --libs glib-2.0` ++LDFLAGS += -L../base/ -L../dynlibsrc/ -L$(HMMER_LIBS) -lpthread `$(PKG_CONFIG) --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- a/src/network/makefile ++++ b/src/network/makefile +@@ -2,9 +2,10 @@ + .SUFFIXES : .dy + + CC = cc ++PKG_CONFIG ?= pkg-config + INCFLAGS = -I../base/ -I../socket -I../dynlibsrc -I../dnaindex +-CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `pkg-config --cflags glib-2.0` +-LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `pkg-config --libs glib-2.0` ++CFLAGS += $(CPPFLAGS) -c -pthread -DUNIX -I../base/ -I../socket -I../dynlibsrc -I../dnaindex `$(PKG_CONFIG) --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../socket -L../dynlibsrc -L../dnaindex -lm `$(PKG_CONFIG) --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- a/src/other_programs/makefile ++++ b/src/other_programs/makefile +@@ -3,8 +3,9 @@ + .SUFFIXES : .dy + + CC = cc +-CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `pkg-config --cflags glib-2.0` +-LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `pkg-config --libs glib-2.0` ++PKG_CONFIG ?= pkg-config ++CFLAGS += $(CPPFLAGS) -g3 -c -pthread -DUNIX -I../base/ -I../dynlibsrc `$(PKG_CONFIG) --cflags glib-2.0` ++LDFLAGS += -g -L../base/ -L../dynlibsrc -lm `$(PKG_CONFIG) --libs glib-2.0` + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 +--- a/src/snp/makefile ++++ b/src/snp/makefile +@@ -3,11 +3,12 @@ + + + CC = cc ++PKG_CONFIG ?= pkg-config + #CFLAGS = -c -O2 -pg -I../base/ -I../dynlibsrc/ + #CFLAGS = -c -O2 -DPTHREAD -DHAS_PTHREAD_SETSCOPE -DUNIX -I../base/ -I../dynlibsrc/ -I. +-CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `pkg-config --cflags glib-2.0` ++CFLAGS += $(CPPFLAGS) -c -g3 -DUNIX -I../base/ -I../dynlibsrc/ -I. -pthread `$(PKG_CONFIG) --cflags glib-2.0` + +-LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `pkg-config --libs glib-2.0` -lpthread -lm ++LDFLAGS += -g -L../base/ -L../dynlibsrc/ -lpthread `$(PKG_CONFIG) --libs glib-2.0` -lpthread -lm + AR_OPTIONS = ru + + RANLIB_NEEDED = 0 diff --git a/academic/wise/patches/spelling.patch b/academic/wise/patches/spelling.patch new file mode 100644 index 0000000000..cb46f070ce --- /dev/null +++ b/academic/wise/patches/spelling.patch @@ -0,0 +1,702 @@ +Author: Andreas Tille <tille@debian.org> +Last-Update: Fri, 22 Sep 2017 09:18:47 +0200 +Description: Fix spelling issues + +--- a/src/dynlibsrc/hscore.c ++++ b/src/dynlibsrc/hscore.c +@@ -413,7 +413,7 @@ DataScore * new_DataScore_from_storage(H + if( hs->st_len == 0 ) { + new = new_DataScoreStorage(); + if( new == NULL ) { +- warn("could not make inital data score storage!"); ++ warn("could not make initial data score storage!"); + return NULL; + } + add_st_Hscore(hs,new); +--- a/src/dynlibsrc/hscore.dy ++++ b/src/dynlibsrc/hscore.dy +@@ -422,7 +422,7 @@ DataScore * new_DataScore_from_storage(H + if( hs->st_len == 0 ) { + new = new_DataScoreStorage(); + if( new == NULL ) { +- warn("could not make inital data score storage!"); ++ warn("could not make initial data score storage!"); + return NULL; + } + add_st_Hscore(hs,new); +--- a/docs/dynamite.tex ++++ b/docs/dynamite.tex +@@ -2839,7 +2839,7 @@ needs at least one offset to be non zero + Once all the semantics of the Dynamite blueprint is ok, the compiler then turns its + attention to the calc lines. This is like a mini-parser operating inside the dynamite + parser, but unlike the dynamite parser, this once was written in yacc/lex and is +-a more vanilla parser enviroment. ++a more vanilla parser environment. + + \subsubsection{Parser Syntax error on calc line} + +--- a/docs/wise2.tex ++++ b/docs/wise2.tex +@@ -121,7 +121,7 @@ Warning Error + Could not read a GeneFrequency file in human.gf + ... + \end{verbatim} +-This means that the enviroment variable WISECONFIGDIR has not been ++This means that the environment variable WISECONFIGDIR has not been + set up correctly. You need to find where the distribution was downloaded + to (a directory called something like wise2.1.16b) and inside that + directory should be the configuration directory wisecfg. You need to +@@ -427,7 +427,7 @@ sequence flag) as well. An example run w + \begin{verbatim} + genewisedb -pfam Pfam -dnas myseq.fa + \end{verbatim} +-If you have set up the HMMER package to work with Pfam using the enviroment ++If you have set up the HMMER package to work with Pfam using the environment + variable HMMERDB, Wise2 will also pick that up as well. + + +@@ -675,7 +675,7 @@ mathematically it is almost that easy: t + of the probability. + + Perhaps a better known example is the relationship between the old +-profile technology, as developped by Gribskov and Gibson along with ++profile technology, as developed by Gribskov and Gibson along with + others, and its probabilistic partner, profile Hidden Markov Models + (profile HMMs). In terms of the actual algorithm these two methods + are very similar: it is simply that the profile HMM has a strong +@@ -1639,7 +1639,7 @@ Of course there are many options to chan + \subsection{dba - Dna Block Aligner} + \label{sec:dba} + +-dba - standing for Dna Block Aligner, was developped by Niclas Jareborg, ++dba - standing for Dna Block Aligner, was developed by Niclas Jareborg, + Richard Durbin and Ewan Birney for characterising shared regulatory regions + of genomic DNA, either in upstream regions or introns of genes + +--- a/src/base/wisefile.c ++++ b/src/base/wisefile.c +@@ -329,7 +329,7 @@ FILE * openfile(const char * filename,co + * + * + * +- * Arg: envname [READ ] enviroment variable to read from [NullString] ++ * Arg: envname [READ ] environment variable to read from [NullString] + * Arg: filename [UNKN ] Undocumented argument [char *] + * Arg: name [READ ] filename to open [NullString] + * Arg: env [UNKN ] Undocumented argument [char *] +@@ -344,17 +344,17 @@ FILE * envopenfile(char * filename,char + char path [512]; + + if( filename == NULL || env == NULL ) { +- warn("Passed a NULL filename or enviroment name into Envfile. Should trap this elsewhere"); ++ warn("Passed a NULL filename or environment name into Envfile. Should trap this elsewhere"); + return NULL; + } + + if( (envp = getenv(env)) == NULL ) { +- /* fail gracefully - somebody might query a number of enviroment variables */ ++ /* fail gracefully - somebody might query a number of environment variables */ + return NULL; + } + + if( strlen(filename) + strlen(envp) < 490 ) { +- warn("Really long filename/enviroment variables [%s] [%s] Can't cope!",filename,envp); ++ warn("Really long filename/environment variables [%s] [%s] Can't cope!",filename,envp); + return NULL; + } + sprintf(path,"%s/%s",filename,envp); +--- a/src/base/wisefile.dy ++++ b/src/base/wisefile.dy +@@ -302,7 +302,7 @@ in HMMer2. You call it as + + %arg + name r filename to open +-envname r enviroment variable to read from ++envname r environment variable to read from + return a valid file pointer or NULL + %% + FILE * envopenfile(char * filename,char * env) +@@ -311,17 +311,17 @@ FILE * envopenfile(char * filename,char + char path [512]; + + if( filename == NULL || env == NULL ) { +- warn("Passed a NULL filename or enviroment name into Envfile. Should trap this elsewhere"); ++ warn("Passed a NULL filename or environment name into Envfile. Should trap this elsewhere"); + return NULL; + } + + if( (envp = getenv(env)) == NULL ) { +- /* fail gracefully - somebody might query a number of enviroment variables */ ++ /* fail gracefully - somebody might query a number of environment variables */ + return NULL; + } + + if( strlen(filename) + strlen(envp) < 490 ) { +- warn("Really long filename/enviroment variables [%s] [%s] Can't cope!",filename,envp); ++ warn("Really long filename/environment variables [%s] [%s] Can't cope!",filename,envp); + return NULL; + } + sprintf(path,"%s/%s",filename,envp); +--- a/src/base/wisefile.h ++++ b/src/base/wisefile.h +@@ -143,7 +143,7 @@ FILE * Wise2_openfile(const char * filen + * + * + * +- * Arg: envname [READ ] enviroment variable to read from [NullString] ++ * Arg: envname [READ ] environment variable to read from [NullString] + * Arg: filename [UNKN ] Undocumented argument [char *] + * Arg: name [READ ] filename to open [NullString] + * Arg: env [UNKN ] Undocumented argument [char *] +--- a/LICENSE ++++ b/LICENSE +@@ -19,7 +19,7 @@ an acknowledgement of the authorship nee + + The HMMer2 libaries (Sean Eddy's HMM package) and the models directory + (The algorithms for the Wise2 package, and final executable programs) +-are both distributed under a Gnu General Public License (GPL). This ++are both distributed under a GNU General Public License (GPL). This + means that the entire package as it is distributed with these portions + in is also licensed under GPL, due to the 'infectious' nature of the + GPL. +--- a/docs/wise3arch.tex ++++ b/docs/wise3arch.tex +@@ -49,7 +49,7 @@ clear up a considerable amount of confus + + \subsection{Committment to open source, freely available code} + +-The Wise2 package has been licensed under the Gnu Public License since ++The Wise2 package has been licensed under the GNU General Public License since + its inception. In addition, parts of the package has even less + restrictive Licenses. I have a strong committment to keep Wise a + freely available, open source package. The aim of the open +--- a/src/corba/scanwise_protein_index.c ++++ b/src/corba/scanwise_protein_index.c +@@ -19,7 +19,7 @@ char * program_name = "scanwise_protein_ + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/assembly/badkmer.c ++++ b/src/dnaindex/assembly/badkmer.c +@@ -25,7 +25,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EBI 2003\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/assembly/pathwise.c ++++ b/src/dnaindex/assembly/pathwise.c +@@ -40,7 +40,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EBI 2003\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/bigseqwise.c ++++ b/src/dnaindex/bigseqwise.c +@@ -10,7 +10,7 @@ char * program_name = "bigseqwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/findbad_kmer.c ++++ b/src/dnaindex/findbad_kmer.c +@@ -13,7 +13,7 @@ char * program_name = "findbad_kmer"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/dnaindex/kwise.c ++++ b/src/dnaindex/kwise.c +@@ -15,7 +15,7 @@ char * program_name = "kwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/alignwise.c ++++ b/src/models/alignwise.c +@@ -61,7 +61,7 @@ void show_Gene_debug(AlnBlock * alb,Sequ + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/amplimer_resolver.c ++++ b/src/models/amplimer_resolver.c +@@ -10,7 +10,7 @@ char * program_name = "amplimer_resolver + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/cdnawise.c ++++ b/src/models/cdnawise.c +@@ -15,7 +15,7 @@ void show_version(FILE * ofp) + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); + + +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL (2001) and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/clonewise.c ++++ b/src/models/clonewise.c +@@ -25,7 +25,7 @@ int mismatch_score = -1; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/dbac.c ++++ b/src/models/dbac.c +@@ -363,7 +363,7 @@ void show_version(FILE * ofp) + fprintf(ofp," Released %s\n",RELEASE_DAY); + fprintf(ofp," Compiled %s\n",COMPILE_DATE); + fprintf(ofp,"dba was written by Niclas Jareborg, Ewan Birney and Richard Durbin\n"); +- fprintf(ofp,"Copyright (c) 1998,1999,2000,2001 GRL ltd. It is distributed under a Gnu Public License\n"); ++ fprintf(ofp,"Copyright (c) 1998,1999,2000,2001 GRL ltd. It is distributed under a GNU General Public License\n"); + fprintf(ofp,"See GNULICENSE in source directory for more information\n"); + } + +--- a/src/models/dnal.c ++++ b/src/models/dnal.c +@@ -104,7 +104,7 @@ void show_short_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/dnawise.c ++++ b/src/models/dnawise.c +@@ -8,7 +8,7 @@ char * program_name = "dnawise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/editdist.c ++++ b/src/models/editdist.c +@@ -8,7 +8,7 @@ char * program_name = "editdist"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/estwise.c ++++ b/src/models/estwise.c +@@ -557,7 +557,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/estwisedb.c ++++ b/src/models/estwisedb.c +@@ -807,7 +807,7 @@ boolean show_header(FILE * ofp) + fprintf(ofp,"-------------------------------------------------------------\n"); + fprintf(ofp,"Wise2 - database searching mode\n"); + fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY); +- fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n"); ++ fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n"); + fprintf(ofp," See -version for more info on copyright\n"); + fprintf(ofp,"Bugs and credits to Ewan Birney <birney@sanger.ac.uk>\n"); + fprintf(ofp,"-------------------------------------------------------------\n\n"); +@@ -836,7 +836,7 @@ boolean show_header(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/evopairwise.c ++++ b/src/models/evopairwise.c +@@ -15,7 +15,7 @@ char * program_name = "evopairwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/fivestar.c ++++ b/src/models/fivestar.c +@@ -14,7 +14,7 @@ char * program_name = "fivestar"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/fivestarscan.c ++++ b/src/models/fivestarscan.c +@@ -14,7 +14,7 @@ char * program_name = "fivestarscan"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/fivestarsearch.c ++++ b/src/models/fivestarsearch.c +@@ -12,7 +12,7 @@ char * program_name = "fivestarsearch"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/genewise.c ++++ b/src/models/genewise.c +@@ -858,7 +858,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/genewisedb.c ++++ b/src/models/genewisedb.c +@@ -505,7 +505,7 @@ boolean show_header(FILE * ofp) + { + fprintf(ofp,"Wise2 - database searching mode\n"); + fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY); +- fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n"); ++ fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n"); + fprintf(ofp," See -version for more info on copyright\n"); + fprintf(ofp,"Bugs and credits to Ewan Birney <birney@sanger.ac.uk>\n"); + fprintf(ofp,"-----------------------------------------------------\n\n"); +@@ -1003,7 +1003,7 @@ void show_help(FILE * ofp) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/genomewise.c ++++ b/src/models/genomewise.c +@@ -16,7 +16,7 @@ void show_utr_exon_genomewise(AlnBlock * + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/lba.c ++++ b/src/models/lba.c +@@ -8,7 +8,7 @@ char * program_name = "lba"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/motifcluster.c ++++ b/src/models/motifcluster.c +@@ -8,7 +8,7 @@ char * program_name = "motifcluster"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/motifdiff.c ++++ b/src/models/motifdiff.c +@@ -8,7 +8,7 @@ char * program_name = "motifdiff"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/motifwise.c ++++ b/src/models/motifwise.c +@@ -8,7 +8,7 @@ char * program_name = "motifwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/oldpostwise.c ++++ b/src/models/oldpostwise.c +@@ -375,7 +375,7 @@ void show_help(char * help_arg) + void show_version(void) + { + fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(stdout,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(stdout,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(stdout,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(stdout,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(stdout,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/promotercluster.c ++++ b/src/models/promotercluster.c +@@ -7,7 +7,7 @@ char * program_name = "promotercluster"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/promoterwise.c ++++ b/src/models/promoterwise.c +@@ -15,7 +15,7 @@ char * program_name = "promoterwise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/pseudowise.c ++++ b/src/models/pseudowise.c +@@ -13,7 +13,7 @@ char * program_name = "pseudowise"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/psw.c ++++ b/src/models/psw.c +@@ -259,7 +259,7 @@ int main(int argc,char ** argv) + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) GRL 1998 and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/pswdb.c ++++ b/src/models/pswdb.c +@@ -95,7 +95,7 @@ void show_help(FILE * ofp) + void show_version(void) + { + fprintf(stdout,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(stdout,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(stdout,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(stdout,"The source code is copyright (c) EMBL 1998 and others\n"); + fprintf(stdout,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(stdout,"For more information read the GNULICENSE file in the distribution\n\n"); +@@ -347,7 +347,7 @@ boolean show_header(FILE * ofp) + fprintf(ofp,"-------------------------------------------------------------\n"); + fprintf(ofp,"Wise2 - Protein vs. Protein\n"); + fprintf(ofp,"Program: %s version: %s released: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY); +- fprintf(ofp,"This program is freely distributed under a Gnu Public License.\n"); ++ fprintf(ofp,"This program is freely distributed under a GNU General Public License.\n"); + fprintf(ofp," See -version for more info on copyright\n"); + fprintf(ofp,"Bugs and credits to: Richard Copley <copley@embl-heidelberg.de>\n"); + fprintf(ofp," Ewan Birney <birney@sanger.ac.uk>\n"); +--- a/src/models/scanwisep.c ++++ b/src/models/scanwisep.c +@@ -421,7 +421,7 @@ HitList * HitList_from_HSP_HSP2HitListIm + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/statwise.c ++++ b/src/models/statwise.c +@@ -11,7 +11,7 @@ char * codon_table = "codon.table"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/models/sywise.c ++++ b/src/models/sywise.c +@@ -12,7 +12,7 @@ char * codon_table = "codon.table"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/network/wise_proteinindex_server.c ++++ b/src/network/wise_proteinindex_server.c +@@ -26,7 +26,7 @@ char * program_name = "scanwise_server"; + void show_version(FILE * ofp) + { + fprintf(ofp,"%s\nVersion: %s\nReleased: %s\nCompiled: %s\n",program_name,VERSION_NUMBER,RELEASE_DAY,COMPILE_DATE); +- fprintf(ofp,"\nThis program is freely distributed under a Gnu Public License\n"); ++ fprintf(ofp,"\nThis program is freely distributed under a GNU General Public License\n"); + fprintf(ofp,"The source code is copyright (c) EMBL and others\n"); + fprintf(ofp,"There is no warranty, implied or otherwise on the performance of this program\n"); + fprintf(ofp,"For more information read the GNULICENSE file in the distribution\n\n"); +--- a/src/test/estwise-db.out ++++ b/src/test/estwise-db.out +@@ -1,7 +1,7 @@ + ------------------------------------------------------------- + Wise2 - database searching mode + Program: estwisedb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to Ewan Birney <birney@sanger.ac.uk> + ------------------------------------------------------------- +--- a/src/test/genewise-db-lite.out ++++ b/src/test/genewise-db-lite.out +@@ -1,6 +1,6 @@ + Wise2 - database searching mode + Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to Ewan Birney <birney@sanger.ac.uk> + ----------------------------------------------------- +--- a/src/test/genewise-db.out ++++ b/src/test/genewise-db.out +@@ -1,6 +1,6 @@ + Wise2 - database searching mode + Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to Ewan Birney <birney@sanger.ac.uk> + ----------------------------------------------------- +--- a/src/test/genewisedb-pfam.out ++++ b/src/test/genewisedb-pfam.out +@@ -1,6 +1,6 @@ + Wise2 - database searching mode + Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to Ewan Birney <birney@sanger.ac.uk> + ----------------------------------------------------- +--- a/src/test/pswdb.out ++++ b/src/test/pswdb.out +@@ -1,7 +1,7 @@ + ------------------------------------------------------------- + Wise2 - Protein vs. Protein + Program: pswdb version: $Name: wise2-4-1 $ released: unreleased +-This program is freely distributed under a Gnu Public License. ++This program is freely distributed under a GNU General Public License. + See -version for more info on copyright + Bugs and credits to: Richard Copley <copley@embl-heidelberg.de> + Ewan Birney <birney@sanger.ac.uk> +--- a/src/models/genefrequency.c ++++ b/src/models/genefrequency.c +@@ -636,7 +636,7 @@ double double_from_line(char * buffer) + ret = strtod(runner,&end); + + if( end == runner || isalnum((int)*end) ) { +- warn("Bad conversion of string [%s] to double [%f] occured",runner,ret); ++ warn("Bad conversion of string [%s] to double [%f] occurred",runner,ret); + } + + return ret; +--- a/src/models/genefrequency.dy ++++ b/src/models/genefrequency.dy +@@ -597,7 +597,7 @@ double double_from_line(char * buffer) + ret = strtod(runner,&end); + + if( end == runner || isalnum((int)*end) ) { +- warn("Bad conversion of string [%s] to double [%f] occured",runner,ret); ++ warn("Bad conversion of string [%s] to double [%f] occurred",runner,ret); + } + + return ret; +--- a/src/models/seqerror.dy ++++ b/src/models/seqerror.dy +@@ -42,7 +42,7 @@ Sequence * seq + SequenceErrorSet * ses + %info + This holds a sequence and what +-errors have occured in it. ++errors have occurred in it. + %% + + +--- a/src/models/seqerror.h ++++ b/src/models/seqerror.h +@@ -72,7 +72,7 @@ typedef struct Wise2_SequenceErrorSet Wi + /* Object ErrorSequence + * + * Descrip: This holds a sequence and what +- * errors have occured in it. ++ * errors have occurred in it. + * + * + */ diff --git a/academic/wise/slack-desc b/academic/wise/slack-desc new file mode 100644 index 0000000000..c99b9025f0 --- /dev/null +++ b/academic/wise/slack-desc @@ -0,0 +1,19 @@ +# HOW TO EDIT THIS FILE: +# The "handy ruler" below makes it easier to edit a package description. +# Line up the first '|' above the ':' following the base package name, and +# the '|' on the right side marks the last column you can put a character in. +# You must make exactly 11 lines for the formatting to be correct. It's also +# customary to leave one space after the ':' except on otherwise blank lines. + + |-----handy-ruler------------------------------------------------------| +wise: wise (Compare protein to DNA sequence) +wise: +wise: Wise compares a protein sequence to a genomic DNA sequence, +wise: allowing for introns and frameshifting errors. +wise: +wise: https://www.ebi.ac.uk/~birney/wise2/ +wise: https://www.ebi.ac.uk/Tools/psa/genewise/ +wise: +wise: +wise: +wise: diff --git a/academic/wise/wise.SlackBuild b/academic/wise/wise.SlackBuild new file mode 100644 index 0000000000..84230832be --- /dev/null +++ b/academic/wise/wise.SlackBuild @@ -0,0 +1,131 @@ +#!/bin/bash + +# Slackware build script for <wise> + +# Copyright 2023 Petar Petrov, slackalaxy@gmail.com +# All rights reserved. +# +# Redistribution and use of this script, with or without modification, is +# permitted provided that the following conditions are met: +# +# 1. Redistributions of this script must retain the above copyright +# notice, this list of conditions and the following disclaimer. +# +# THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED +# WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +# MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO +# EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, +# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; +# OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, +# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR +# OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF +# ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + +cd $(dirname $0) ; CWD=$(pwd) + +PRGNAM=wise +VERSION=${VERSION:-2.4.1} +BUILD=${BUILD:-2} +TAG=${TAG:-_SBo} +PKGTYPE=${PKGTYPE:-tgz} + +if [ -z "$ARCH" ]; then + case "$( uname -m )" in + i?86) ARCH=i586 ;; + arm*) ARCH=arm ;; + *) ARCH=$( uname -m ) ;; + esac +fi + +if [ ! -z "${PRINT_PACKAGE_NAME}" ]; then + echo "$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE" + exit 0 +fi + +TMP=${TMP:-/tmp/SBo} +PKG=$TMP/package-$PRGNAM +OUTPUT=${OUTPUT:-/tmp} + +if [ "$ARCH" = "i586" ]; then + SLKCFLAGS="-O2 -march=i586 -mtune=i686" +elif [ "$ARCH" = "i686" ]; then + SLKCFLAGS="-O2 -march=i686 -mtune=i686" +elif [ "$ARCH" = "x86_64" ]; then + SLKCFLAGS="-O2 -fPIC" +else + SLKCFLAGS="-O2" +fi + +set -e + +rm -rf $PKG +mkdir -p $TMP $PKG $OUTPUT +cd $TMP +rm -rf $PRGNAM-$VERSION +tar xvf $CWD/${PRGNAM}_${VERSION}.orig.tar.gz +cd $PRGNAM-$VERSION +chown -R root:root . +find -L . \ + \( -perm 777 -o -perm 775 -o -perm 750 -o -perm 711 -o -perm 555 \ + -o -perm 511 \) -exec chmod 755 {} \; -o \ + \( -perm 666 -o -perm 664 -o -perm 640 -o -perm 600 -o -perm 444 \ + -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \; + +patch -p1 -i $CWD/patches/01_welcome-csh.patch +patch -p1 -i $CWD/patches/02_isnumber.patch +patch -p1 -i $CWD/patches/03_doc-nodycache.patch +patch -p1 -i $CWD/patches/04_wise2-pdflatex-update.patch +patch -p1 -i $CWD/patches/05_glib2.patch +patch -p1 -i $CWD/patches/06_getline.patch +patch -p1 -i $CWD/patches/07_ld--as-needed.patch +patch -p1 -i $CWD/patches/08_mayhem.patch +patch -p1 -i $CWD/patches/09_dnal-add-return-statement.patch +patch -p1 -i $CWD/patches/10_fix_path_to_data_files.patch +patch -p1 -i $CWD/patches/11_consistent_manual_dates.patch +patch -p1 -i $CWD/patches/spelling.patch +patch -p1 -i $CWD/patches/cross.patch + +# This prevents some weird build breaks. Thanks to Urchlay. His explanation: +# +# The .c files that are in the tarball, were already built from the .dy +# files. However, some of them get patched, e.g. wisefile.c and wisefile.dy +# both have a modification time of the current time/date, which is why make +# thinks it needs to rebuild the wisefile.c. When make is run, it looks at +# the timestamps and decided wisefile.c is older than wisefile.dy (which it +# is, ever so slightly, assuming the filesystem's timestamp resolution is +# fine enough). What the solution does is force the timestamp on all the +# .dy files to be older than the generated .c files, so make won't think it +# needs to run dyc to generate the .c files. +find src -name \*.dy -print0 | xargs -0 touch -d '2000-01-01' + +cd src +CFLAGS="$SLKCFLAGS" \ +CXXFLAGS="$SLKCFLAGS" \ +make all + +mkdir -p $PKG/usr/bin +mkdir -p $PKG/usr/share/$PRGNAM + +cd bin +for i in * ; do + install -m 755 $i $PKG/usr/bin/$i +done + +cd ../.. +cp -a test_data wisecfg/* $PKG/usr/share/$PRGNAM + +find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \ + | cut -f 1 -d : | xargs strip --strip-unneeded 2> /dev/null || true + +mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION +cp -a \ + LICENSE README docs/{*.tex,*.eps,papers} \ + $PKG/usr/doc/$PRGNAM-$VERSION +cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild + +mkdir -p $PKG/install +cat $CWD/slack-desc > $PKG/install/slack-desc + +cd $PKG +/sbin/makepkg -l y -c n $OUTPUT/$PRGNAM-$VERSION-$ARCH-$BUILD$TAG.$PKGTYPE diff --git a/academic/wise/wise.info b/academic/wise/wise.info new file mode 100644 index 0000000000..1aafd927ee --- /dev/null +++ b/academic/wise/wise.info @@ -0,0 +1,10 @@ +PRGNAM="wise" +VERSION="2.4.1" +HOMEPAGE="https://www.ebi.ac.uk/Tools/psa/genewise/" +DOWNLOAD="http://deb.debian.org/debian/pool/main/w/wise/wise_2.4.1.orig.tar.gz" +MD5SUM="9e90132c19a653831ce63b5af7f08302" +DOWNLOAD_x86_64="" +MD5SUM_x86_64="" +REQUIRES="" +MAINTAINER="Petar Petrov" +EMAIL="slackalaxy@gmail.com" |