diff options
| -rw-r--r-- | academic/tophat/fix_build_w_seqan1.4.patch | 24 | ||||
| -rw-r--r-- | academic/tophat/tophat.SlackBuild | 24 | ||||
| -rw-r--r-- | academic/tophat/tophat.info | 6 |
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="" |