From fe3095faf885d66e39a7cf0ff242dce6b3353aef Mon Sep 17 00:00:00 2001 From: Petar Petrov Date: Sun, 19 Feb 2012 14:20:37 -0600 Subject: academic/staden: Several fixes/enhancements I notified upstream that Staden had been added to SlackBuilds.org and got some handy tips. So: 1) The components of the program will now find their documentation directly. 2) The Staden package is now ready to provide a GUI for EMBOSS. 3) The real icons are used (converted from their Mac format). Signed-off-by: Robby Workman --- academic/staden/README | 36 ++++++++++++++++++-------------- academic/staden/desktop/gap4.desktop | 2 +- academic/staden/desktop/gap4.png | Bin 0 -> 2970 bytes academic/staden/desktop/gap5.desktop | 2 +- academic/staden/desktop/gap5.png | Bin 0 -> 2970 bytes academic/staden/desktop/pregap4.desktop | 2 +- academic/staden/desktop/pregap4.png | Bin 0 -> 31200 bytes academic/staden/desktop/spin.desktop | 2 +- academic/staden/desktop/spin.png | Bin 0 -> 31200 bytes academic/staden/desktop/trev.desktop | 2 +- academic/staden/desktop/trev.png | Bin 0 -> 25610 bytes academic/staden/staden.SlackBuild | 27 +++++++++++++++--------- academic/staden/staden.png | Bin 3953 -> 0 bytes 13 files changed, 42 insertions(+), 31 deletions(-) create mode 100644 academic/staden/desktop/gap4.png create mode 100644 academic/staden/desktop/gap5.png create mode 100644 academic/staden/desktop/pregap4.png create mode 100644 academic/staden/desktop/spin.png create mode 100644 academic/staden/desktop/trev.png delete mode 100644 academic/staden/staden.png diff --git a/academic/staden/README b/academic/staden/README index 58460934c6..ccb3223dcf 100644 --- a/academic/staden/README +++ b/academic/staden/README @@ -2,26 +2,30 @@ The programs part of the Staden package provide a fully developed set of DNA sequence assembly, editing, analysis and more. Some of its features include: -GAP4 - Performs assembly, contig joining, assembly checking, repeat search, - experiment suggestion, read pair analysis and contig editing. -GAP5 - The new development version of Gap4, designed to work with the large - volumes of data attainable through the newer sequencing technologies. -PREGAP4 - Provides a graphical user interface to set up the processing - required to prepare trace data for assembly or analysis. -SPIN - Compares pairs of sequences in many ways, often presenting its results - graphically and has a sliding sequence window linked to the plots. -TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF trace files. +GAP4 - Performs assembly, contig joining, assembly checking, repeat + search, experiment suggestion, read pair analysis and contig + editing. +GAP5 - The new development version of Gap4, designed to work with the + large volumes of data attainable through the newer sequencing + technologies. +PREGAP4 - Provides a graphical user interface to set up the processing + required to prepare trace data for assembly or analysis. +SPIN - Compares pairs of sequences in many ways, often presenting its + results graphically and has a sliding sequence window linked to + the plots. +TREV - A rapid and flexible viewer and editor for ABI, ALF or SCF + trace files. -For more information and citing, visit Staden's web page and check the +For more information and citing, visit Staden's web page and check the "References" file in the documentation. This requires io_lib and tklib. Notes: 1) You should run the SlackBuild in real root environment (su -)! -2) Make sure you have Emacs and Tetex installed, as they are needed - to generate the documentation. -3) Slackware's TCL and TK sources are expected to be in /tmp at build - time. The SlackBuild will unpack them in the build directory and - create the necessary symlinks in /tmp. You can safely delete the - symlinks when the build is complete. +2) Make sure you have Emacs and Tetex installed at build time. +3) Although unsupported at the moment, SPIN can provide a GUI for the + EMBOSS suite programs. If you want to give it a try, run as root + "create_emboss_data" (EMBOSS should be installed, of course). This + generates some files in /usr/share/staden/tcl/spin_emboss/acdtcl, + so remember to manually clean them if you later uninstall staden. diff --git a/academic/staden/desktop/gap4.desktop b/academic/staden/desktop/gap4.desktop index 1a07a8a378..e0200a38d5 100644 --- a/academic/staden/desktop/gap4.desktop +++ b/academic/staden/desktop/gap4.desktop @@ -1,7 +1,7 @@ [Desktop Entry] Categories=Education; Exec=gap4 -Icon=staden +Icon=gap4 Name=Staden Package GAP4 StartupNotify=false Type=Application diff --git a/academic/staden/desktop/gap4.png b/academic/staden/desktop/gap4.png new file mode 100644 index 0000000000..98248c7517 Binary files /dev/null and b/academic/staden/desktop/gap4.png differ diff --git a/academic/staden/desktop/gap5.desktop b/academic/staden/desktop/gap5.desktop index 383388c8bb..1901860d3f 100644 --- a/academic/staden/desktop/gap5.desktop +++ b/academic/staden/desktop/gap5.desktop @@ -1,7 +1,7 @@ [Desktop Entry] Categories=Education; Exec=gap5 -Icon=staden +Icon=gap5 Name=Staden Package GAP5 StartupNotify=false Type=Application diff --git a/academic/staden/desktop/gap5.png b/academic/staden/desktop/gap5.png new file mode 100644 index 0000000000..98248c7517 Binary files /dev/null and b/academic/staden/desktop/gap5.png differ diff --git a/academic/staden/desktop/pregap4.desktop b/academic/staden/desktop/pregap4.desktop index 645cf11968..df13c9366e 100644 --- a/academic/staden/desktop/pregap4.desktop +++ b/academic/staden/desktop/pregap4.desktop @@ -1,7 +1,7 @@ [Desktop Entry] Categories=Education; Exec=pregap4 -Icon=staden +Icon=pregap4 Name=Staden Package PREGAP4 StartupNotify=false Type=Application diff --git a/academic/staden/desktop/pregap4.png b/academic/staden/desktop/pregap4.png new file mode 100644 index 0000000000..ad7fbbbe9a Binary files /dev/null and b/academic/staden/desktop/pregap4.png differ diff --git a/academic/staden/desktop/spin.desktop b/academic/staden/desktop/spin.desktop index b220336034..8a9f14926a 100644 --- a/academic/staden/desktop/spin.desktop +++ b/academic/staden/desktop/spin.desktop @@ -1,7 +1,7 @@ [Desktop Entry] Categories=Education; Exec=spin -Icon=staden +Icon=spin Name=Staden Package SPIN StartupNotify=false Type=Application diff --git a/academic/staden/desktop/spin.png b/academic/staden/desktop/spin.png new file mode 100644 index 0000000000..ad7fbbbe9a Binary files /dev/null and b/academic/staden/desktop/spin.png differ diff --git a/academic/staden/desktop/trev.desktop b/academic/staden/desktop/trev.desktop index cc620d24c5..45fa67bce1 100644 --- a/academic/staden/desktop/trev.desktop +++ b/academic/staden/desktop/trev.desktop @@ -1,7 +1,7 @@ [Desktop Entry] Categories=Education; Exec=trev -Icon=staden +Icon=trev Name=Staden Package TREV StartupNotify=false Type=Application diff --git a/academic/staden/desktop/trev.png b/academic/staden/desktop/trev.png new file mode 100644 index 0000000000..c7ae77a0f2 Binary files /dev/null and b/academic/staden/desktop/trev.png differ diff --git a/academic/staden/staden.SlackBuild b/academic/staden/staden.SlackBuild index a950d643ef..707e9007de 100644 --- a/academic/staden/staden.SlackBuild +++ b/academic/staden/staden.SlackBuild @@ -2,7 +2,7 @@ # Slackware build script for staden -# Copyright 2011 Petar Petrov, ppetrov@paju.oulu.fi +# Copyright 2011-2012 Petar Petrov, ppetrov@paju.oulu.fi # All rights reserved. # # Redistribution and use of this script, with or without modification, is @@ -24,7 +24,7 @@ PRGNAM=staden VERSION=${VERSION:-2.0.0b9} -BUILD=${BUILD:-1} +BUILD=${BUILD:-2} TAG=${TAG:-_SBo} if [ -z "$ARCH" ]; then @@ -37,7 +37,7 @@ fi SLKTCL=tcl8.5.9 # Slackware 13.37 sources for TCL SLKTK=tk8.5.9 # Slackware 13.37 sources for TK -TKLIB=tklib0.5 # Folder name of TKLIB libraries, see line 117. +TKLIB=tklib0.5 # Folder name of TKLIB CWD=$(pwd) TMP=${TMP:-/tmp/SBo} @@ -95,6 +95,14 @@ sed -i "s:$STADENROOT/lib:$STADENROOT/lib${LIBDIRSUFFIX}:g" \ prefinish/finish_sanger prefinish/prefinish pregap4/pregap4 spin/spin \ spin_emboss/create_emboss_files trev/trev +# Point to the right place of the EMBOSS .acd and data files. This is +# needed if the "create_emboss_files" script is run after install. +sed -i "133 c set acd_dir /usr/share/EMBOSS/acd" spin_emboss/create_emboss_files.tcl +sed -i "73 a EMBOSS_DATA=/usr/share/EMBOSS/data; export EMBOSS_DATA" spin/spin + +# Correct the path where staden components look for their manual. +sed -i "s:/share/doc/staden/manual:/doc/$PRGNAM-$VERSION/manual:" tk_utils/help_config + CFLAGS="$SLKCFLAGS" \ CXXFLAGS="$SLKCFLAGS" \ ./configure \ @@ -113,7 +121,7 @@ make install DESTDIR=$PKG # Build documentation. In the process, texi2dvi looks for tex and # that's why the SlackBuild should be run as real root (su -). # ## (or just source /etc/profile ) --rworkman -cd ../${PRGNAM}_doc-$VERSION-src +cd $TMP/$PRGNAM-$VERSION/${PRGNAM}_doc-$VERSION-src # Fix the doc and man pages paths sed "s:{datarootdir}/doc/staden:{prefix}/doc/$PRGNAM-$VERSION:" -i Makefile @@ -130,6 +138,9 @@ make install DESTDIR=$PKG # Now that we're done building, let's remove those symlinks from earlier... rm -f /tmp/$SLKTCL /tmp/$SLKTK +# This is empty +rm -rf $PKG/usr/share/doc + 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 @@ -137,17 +148,13 @@ find $PKG/usr/man -type f -exec gzip -9 {} \; for i in $( find $PKG/usr/man -type l ) ; do ln -s $( readlink $i ).gz $i.gz ; rm $i ; done mkdir -p $PKG/usr/share/{applications,pixmaps} -cp $CWD/desktop/* $PKG/usr/share/applications -cp $CWD/$PRGNAM.png $PKG/usr/share/pixmaps +cp $CWD/desktop/*.desktop $PKG/usr/share/applications +cp $CWD/desktop/*.png $PKG/usr/share/pixmaps -mkdir -p $PKG/usr/doc/$PRGNAM-$VERSION cd ../$PRGNAM-$VERSION-src cp -a ChangeLog NEWS README.build $PKG/usr/doc/$PRGNAM-$VERSION cat $CWD/$PRGNAM.SlackBuild > $PKG/usr/doc/$PRGNAM-$VERSION/$PRGNAM.SlackBuild cat $CWD/References > $PKG/usr/doc/$PRGNAM-$VERSION/References -# Staden components expect the manual to be in /usr/share/doc/staden. -ln -s $PRGNAM-$VERSION $PKG/usr/doc/$PRGNAM -rm -rf $PKG/usr/share/doc # This is empty mkdir -p $PKG/install cat $CWD/slack-desc > $PKG/install/slack-desc diff --git a/academic/staden/staden.png b/academic/staden/staden.png deleted file mode 100644 index d57d0e1bcb..0000000000 Binary files a/academic/staden/staden.png and /dev/null differ -- cgit v1.2.3