academic/tophat: Fix Build.

Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>

3 files changed, 48 insertions, 6 deletions

diff --git a/academic/tophat/fix_build_w_seqan1.4.patch b/academic/tophat/fix_build_w_seqan1.4.patch
new file mode 100644
index 0000000000..f51b833c1e
--- /dev/null
+++ b/academic/tophat/fix_build_w_seqan1.4.patch
@@ -0,0 +1,24 @@
+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/tophat.SlackBuild b/academic/tophat/tophat.SlackBuild
index 4d4d306fc8..44ec838590 100644
--- a/academic/tophat/tophat.SlackBuild
+++ b/academic/tophat/tophat.SlackBuild
@@ -62,25 +62,41 @@ 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
 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 {} \;
 
-CFLAGS="$SLKCFLAGS" \
+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" \
 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
 
-make
+sed -i 's|-L/usr/lib||' Makefile src/Makefile
+
+make -j1
 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 e7d9aafd50..221a4dede1 100644
--- a/academic/tophat/tophat.info
+++ b/academic/tophat/tophat.info
@@ -1,8 +1,10 @@
 PRGNAM="tophat"
 VERSION="2.1.0"
 HOMEPAGE="http://ccb.jhu.edu/software/tophat/"
-DOWNLOAD="http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.tar.gz"
-MD5SUM="34afa379b030c6672a31bbe3689745bc"
+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_x86_64=""
 MD5SUM_x86_64=""
 REQUIRES=""