From b6456152b10e4c01ee304557130dc8b19747186a Mon Sep 17 00:00:00 2001
From: Petar Petrov
Date: Sun, 5 Jun 2016 15:51:46 +0300
Subject: academic/tophat: Updated for version 2.1.1

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
---
 academic/tophat/fix_build_w_seqan1.4.patch | 24 ------------------------
 academic/tophat/slack-desc                 |  2 +-
 academic/tophat/tophat.SlackBuild          | 26 +++++---------------------
 academic/tophat/tophat.info                |  8 +++-----
 4 files changed, 9 insertions(+), 51 deletions(-)
 delete mode 100644 academic/tophat/fix_build_w_seqan1.4.patch

(limited to 'academic')

diff --git a/academic/tophat/fix_build_w_seqan1.4.patch b/academic/tophat/fix_build_w_seqan1.4.patch
deleted file mode 100644
index f51b833c1e..0000000000
--- a/academic/tophat/fix_build_w_seqan1.4.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Description: Resolves build failure with seqan 1.4
-Bug-Closed: http://bugs.debian.org/733352
-Author: Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
---- a/src/segment_juncs.cpp
-+++ b/src/segment_juncs.cpp
-@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl
-     typedef map<uint32_t, IntronMotifs> MotifMap;
-     
-     MotifMap ims;
--	
--    seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
--    seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
--    
-+
-+    typedef seqan::ModifiedString<
-+                    seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >,  
-+                    seqan::ModReverse>   ConstDnaStringReverseComplement;
-+    ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
-+    ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
-+     
-     if (talkative)
-         fprintf(stderr, "Collecting potential splice sites in islands\n");
- 
-
diff --git a/academic/tophat/slack-desc b/academic/tophat/slack-desc
index 68f24c83c6..72180b86b6 100644
--- a/academic/tophat/slack-desc
+++ b/academic/tophat/slack-desc
@@ -14,6 +14,6 @@ tophat: high-throughput short read aligner Bowtie, and then analyzes the
 tophat: mapping results to identify splice junctions between exons.
 tophat:
 tophat: Home: http://tophat.cbcb.umd.edu/
-tophat: References: /usr/doc/tophat-2.1.0/References
+tophat: References: /usr/doc/tophat-2.1.1/References
 tophat:
 tophat:
diff --git a/academic/tophat/tophat.SlackBuild b/academic/tophat/tophat.SlackBuild
index d8ae387909..4254c78d6c 100644
--- a/academic/tophat/tophat.SlackBuild
+++ b/academic/tophat/tophat.SlackBuild
@@ -23,7 +23,7 @@
 #  ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 
 PRGNAM=tophat
-VERSION=${VERSION:-2.1.0}
+VERSION=${VERSION:-2.1.1}
 BUILD=${BUILD:-1}
 TAG=${TAG:-_SBo}
 
@@ -62,41 +62,25 @@ cd $TMP
 rm -rf $PRGNAM-$VERSION
 tar xvf $CWD/$PRGNAM-$VERSION.tar.gz
 cd $PRGNAM-$VERSION
-tar xvf $CWD/seqan-v1.4.2.tar.gz || tar xvf $CWD/seqan-seqan-v1.4.2.tar.gz
 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 {} \;
+ -o -perm 440 -o -perm 400 \) -exec chmod 644 {} \;
 
-sed -e 's|-gdwarf-2||' \
-    -e '/define.*esyscmd/d' \
-    -e 's/svnversion/Unversioned directory/' \
-    -i configure.ac
-
-sed -e 's|make $(SAMPROG)|make -e $(SAMPROG)|' \
-    -i src/Makefile.am
-
-# fixes seqan issues, Thanks to ARCH
-rm -rf src/SeqAn-1.3
-patch -p1 < $CWD/fix_build_w_seqan1.4.patch
-sed -e "s|-I./SeqAn-1.3|-I$TMP/$PRGNAM-$VERSION/seqan-seqan-v1.4.2/core/include|" configure.ac
-
-autoreconf -fi
-CFLAGS="$SLKCFLAGS -I$TMP/$PRGNAM-$VERSION/seqan-seqan-v1.4.2/core/include" \
+CFLAGS="$SLKCFLAGS" \
 CXXFLAGS="$SLKCFLAGS" \
 ./configure \
   --prefix=/usr \
   --libdir=/usr/lib${LIBDIRSUFFIX} \
   --sysconfdir=/etc \
+  --with-boost-libdir=/usr/lib${LIBDIRSUFFIX} \
   --localstatedir=/var \
   --mandir=/usr/man \
   --build=$ARCH-slackware-linux
 
-sed -i 's|-L/usr/lib||' Makefile src/Makefile
-
-make -j1
+make
 make install DESTDIR=$PKG
 
 find $PKG -print0 | xargs -0 file | grep -e "executable" -e "shared object" | grep ELF \
diff --git a/academic/tophat/tophat.info b/academic/tophat/tophat.info
index 221a4dede1..32ecba312c 100644
--- a/academic/tophat/tophat.info
+++ b/academic/tophat/tophat.info
@@ -1,10 +1,8 @@
 PRGNAM="tophat"
-VERSION="2.1.0"
+VERSION="2.1.1"
 HOMEPAGE="http://ccb.jhu.edu/software/tophat/"
-DOWNLOAD="http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.tar.gz \
-  	  https://github.com/seqan/seqan/archive/seqan-v1.4.2.tar.gz"
-MD5SUM="34afa379b030c6672a31bbe3689745bc \
-	7b0080b01feeb223e054dabef53d6fc5"
+DOWNLOAD="http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz"
+MD5SUM="4b2391de46457ba6b2b7268a9da593e4"
 DOWNLOAD_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES=""
-- 
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