diff options
| -rw-r--r-- | academic/tophat/fix_build_w_seqan1.4.patch | 24 | ||||
| -rw-r--r-- | academic/tophat/slack-desc | 2 | ||||
| -rw-r--r-- | academic/tophat/tophat.SlackBuild | 26 | ||||
| -rw-r--r-- | academic/tophat/tophat.info | 8 |
4 files changed, 9 insertions, 51 deletions
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="" |