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authorPetar Petrov <slackalaxy@gmail.com>2016-06-05 15:51:46 +0300
committerWilly Sudiarto Raharjo <willysr@slackbuilds.org>2016-06-05 22:28:03 +0700
commitb6456152b10e4c01ee304557130dc8b19747186a (patch)
tree5cbc1a371dc2a1abb0e70cc791c9663607c27c46
parent8f0d485cccc8057929671e36af7a0258be50ea69 (diff)
downloadslackbuilds-b6456152b10e4c01ee304557130dc8b19747186a.tar.gz
academic/tophat: Updated for version 2.1.1
Signed-off-by: Willy Sudiarto Raharjo <willysr@slackbuilds.org>
-rw-r--r--academic/tophat/fix_build_w_seqan1.4.patch24
-rw-r--r--academic/tophat/slack-desc2
-rw-r--r--academic/tophat/tophat.SlackBuild26
-rw-r--r--academic/tophat/tophat.info8
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=""