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author | BioArchLinuxBot | 2023-06-01 21:28:05 +0000 |
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committer | BioArchLinuxBot | 2023-06-01 21:28:05 +0000 |
commit | a727a0369c93b7da216c02d5ece53c8e213f114f (patch) | |
tree | ce26253450a52adfb3b4e16d52b972b8c0acdc41 | |
parent | 4bb5f7f538b0640f41d78651cbef939ac46b91c7 (diff) | |
download | aur-a727a0369c93b7da216c02d5ece53c8e213f114f.tar.gz |
[lilac] updated to 2.1.2-3
-rw-r--r-- | .SRCINFO | 18 | ||||
-rw-r--r-- | PKGBUILD | 50 | ||||
-rw-r--r-- | configure.patch | 19 | ||||
-rw-r--r-- | make_pair.patch | 4 |
4 files changed, 60 insertions, 31 deletions
@@ -1,21 +1,21 @@ -# Generated by mksrcinfo v8 -# Thu Jun 2 09:32:08 UTC 2016 pkgbase = tophat pkgdesc = fast splice junction mapper for RNA-Seq reads - pkgver = 2.1.1 - pkgrel = 2 + pkgver = 2.1.2 + pkgrel = 3 url = http://ccb.jhu.edu/software/tophat/index.shtml arch = x86_64 arch = i686 license = custom makedepends = boost + makedepends = clang depends = boost-libs depends = bowtie2 - depends = python2 - source = http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.tar.gz + depends = python + source = tophat-2.1.2.tar.gz::https://github.com/DaehwanKimLab/tophat/archive/refs/tags/v2.1.2.tar.gz source = make_pair.patch - md5sums = 4b2391de46457ba6b2b7268a9da593e4 - md5sums = 53378885f3620a1d02fb345077609d05 + source = configure.patch + md5sums = db844fd7f53c519e716cd6222e6195b2 + md5sums = 4f53cd3e611c2a0744babede14c3ae66 + md5sums = 175420b0b08f2979d9585ec55cbeb0ee pkgname = tophat - @@ -1,18 +1,21 @@ # Maintainer: Christian Krause ("wookietreiber") <kizkizzbangbang@googlemail.com> pkgname=tophat -pkgver=2.1.1 -pkgrel=2 +pkgver=2.1.2 +pkgrel=3 pkgdesc="fast splice junction mapper for RNA-Seq reads" arch=('x86_64' 'i686') url="http://ccb.jhu.edu/software/tophat/index.shtml" license=('custom') -depends=('boost-libs' 'bowtie2' 'python2') -makedepends=('boost') -source=("http://ccb.jhu.edu/software/tophat/downloads/tophat-$pkgver.tar.gz" - 'make_pair.patch') -md5sums=('4b2391de46457ba6b2b7268a9da593e4' - '53378885f3620a1d02fb345077609d05') +depends=('boost-libs' 'bowtie2' 'python') +makedepends=('boost' 'clang') +source=("${pkgname}-${pkgver}.tar.gz::https://github.com/DaehwanKimLab/tophat/archive/refs/tags/v${pkgver}.tar.gz" + 'make_pair.patch' + 'configure.patch' + ) +md5sums=('db844fd7f53c519e716cd6222e6195b2' + '4f53cd3e611c2a0744babede14c3ae66' + '175420b0b08f2979d9585ec55cbeb0ee') prepare() { cd $srcdir/$pkgname-$pkgver @@ -20,22 +23,28 @@ prepare() { sed -e 's|make $(SAMPROG)|make -e $(SAMPROG)|' \ -i src/Makefile.am - sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \ - -i src/bed_to_juncs \ - src/contig_to_chr_coords \ - src/sra_to_solid \ - src/tophat-fusion-post \ - src/tophat.py + # sed -e 's|#!/usr/bin/env python|#!/usr/bin/env python2|' \ + # -i src/bed_to_juncs \ + # src/contig_to_chr_coords \ + # src/sra_to_solid \ + # src/tophat-fusion-post \ + # src/tophat.py + + # to python3 + 2to3 -w -n . patch -Np1 -i $srcdir/make_pair.patch + patch -Np0 -i $srcdir/configure.patch + autoreconf -i + autoupdate + autoconf } build() { cd $srcdir/$pkgname-$pkgver - - export PYTHON=python2 - - ./configure --prefix=/usr + export CC=clang + export CXX=clang++ + ./configure --prefix=/usr --with-python-sys-prefix # do not link against system-installed libbam.a sed -e 's|-L/usr/lib||' \ @@ -50,9 +59,10 @@ package() { make DESTDIR=$pkgdir install # fix python install - install -d $pkgdir/usr/lib/python2.7/site-packages + _pyver=$(python -V | cut -d ' ' -f2) + install -d $pkgdir/usr/lib/python${_pyver:0:4}/site-packages mv \ - -t $pkgdir/usr/lib/python2.7/site-packages \ + -t $pkgdir/usr/lib/python${_pyver:0:4}/site-packages \ $pkgdir/usr/bin/{intervaltree,sortedcontainers} install -Dm644 LICENSE $pkgdir/usr/share/licenses/$pkgname/LICENSE diff --git a/configure.patch b/configure.patch new file mode 100644 index 000000000000..716b6c003424 --- /dev/null +++ b/configure.patch @@ -0,0 +1,19 @@ +--- configure.ac.bak 2018-05-24 23:24:31.000000000 +0800 ++++ configure.ac 2022-07-19 10:24:36.805405047 +0800 +@@ -5,7 +5,7 @@ + AC_CONFIG_SRCDIR([config.h.in]) + AC_CONFIG_HEADERS([config.h]) + # AC_CONFIG_AUX_DIR([build-aux]) +-AM_INIT_AUTOMAKE ++AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) + + AC_ARG_VAR(PYTHON, [python program]) + +@@ -108,7 +108,6 @@ + CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2" + LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS" + +-AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign]) + + # makefiles to configure + AC_CONFIG_FILES([Makefile src/Makefile]) diff --git a/make_pair.patch b/make_pair.patch index 44b71d1059ab..0ec41903308b 100644 --- a/make_pair.patch +++ b/make_pair.patch @@ -9,14 +9,14 @@ diff -uBw -aur tophat-2.1.1/src/juncs_db.cpp tophat-2.1.1-patched/src/juncs_db.c + junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), JunctionStats())); } } - + diff -uBw -aur tophat-2.1.1/src/tophat_reports.cpp tophat-2.1.1-patched/src/tophat_reports.cpp --- tophat-2.1.1/src/tophat_reports.cpp 2016-02-23 22:20:44.320710000 +0100 +++ tophat-2.1.1-patched/src/tophat_reports.cpp 2016-06-02 11:26:22.057239478 +0200 @@ -2705,7 +2705,7 @@ junction_stat.gtf_match = true; junction_stat.accepted = true; - + - gtf_junctions.insert(make_pair<Junction, JunctionStats>(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); + gtf_junctions.insert(make_pair(Junction(ref_id, left_coord, right_coord, antisense), junction_stat)); } |