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sci-biology/tophat: remove last-rited package

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Signed-off-by: Mikle Kolyada <zlogene@gentoo.org>
This commit is contained in:
Mikle Kolyada
2020-02-28 10:30:13 +03:00
parent b4185f9dfe
commit c22df03ee4
6 changed files with 0 additions and 310 deletions
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1
sci-biology/tophat/Manifest
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@@ -1 +0,0 @@
DIST tophat-2.1.1.tar.gz 2259554 BLAKE2B f01b08cc2046b7d143864d64aa3e34d3000c7c10d7e50a4e102d500556e8620996de03392463f9d08ae97858eaec85b2df3b5d5ee5b0b4f7a5c0ae06bb3d08e8 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc

14
sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch
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@@ -1,14 +0,0 @@
Fix building with C++14, which errors out due to broken perfect forwarding signature.
See also: https://bugs.gentoo.org/show_bug.cgi?id=594544
--- a/src/tophat_reports.cpp
+++ b/src/tophat_reports.cpp
@@ -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));
}
}
fprintf(stderr, "Loaded %d GFF junctions from %s.\n", (int)(gtf_junctions.size()), gtf_juncs.c_str());

42
sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch
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@@ -1,42 +0,0 @@
Make Python 2 explicit in python scripts
--- a/src/bed_to_juncs
+++ b/src/bed_to_juncs
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
# encoding: utf-8
"""
bed_to_juncs.py
--- a/src/contig_to_chr_coords
+++ b/src/contig_to_chr_coords
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
# encoding: utf-8
"""
contig_to_chr_coords.py
--- a/src/sra_to_solid
+++ b/src/sra_to_solid
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
"""
sra_to_solid.py
--- a/src/tophat-fusion-post
+++ b/src/tophat-fusion-post
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
"""
--- a/src/tophat.py
+++ b/src/tophat.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python2
# encoding: utf-8
"""

162
sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch
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@@ -1,162 +0,0 @@
Unbundle the included samtools and SeqAn, and use system libraries.
See also: https://bugs.gentoo.org/show_bug.cgi?id=566494
Remove ancient ax_boost_base.m4 and ax_boost_thread.m4, and depend
on >=sys-devel/autoconf-archive-2016.09.16 in the ebuild instead.
See also: https://bugs.gentoo.org/show_bug.cgi?id=594810
--- a/configure.ac
+++ b/configure.ac
@@ -28,26 +28,15 @@
AC_PROG_INSTALL
AM_PATH_PYTHON([2.4])
-m4_include([ax_boost_base.m4])
-m4_include([ax_boost_thread.m4])
# CXXFLAGS="$CXXFLAGS $threadLib"
AX_BOOST_BASE([1.38.0])
+AX_BOOST_SYSTEM
AX_BOOST_THREAD
-if test -z "$BOOST_THREAD_LIBS"; then
+if test -z "$BOOST_THREAD_LIB"; then
AC_MSG_ERROR([boost.thread not found. Aborting.])
fi
-# BAM related:
- ac_bam_path=samtools-0.1.18
- BAM_LIB="-lbam"
- BAM_LDFLAGS="-L./$ac_bam_path"
- BAM_CPPFLAGS="-I./$ac_bam_path"
- AC_SUBST(BAM_CPPFLAGS)
- AC_SUBST(BAM_LDFLAGS)
- AC_SUBST(BAM_LIB)
-
-
# Checks for header files.
AC_CHECK_HEADERS([stdlib.h string.h unistd.h])
@@ -80,32 +69,23 @@
# set CFLAGS and CXXFLAGS
#user_CFLAGS="${CXXFLAGS}"
user_CFLAGS=${CFLAGS}
-generic_CFLAGS="-Wall -Wno-strict-aliasing -g -gdwarf-2 -Wuninitialized"
+generic_CFLAGS=""
ext_CFLAGS=""
debug_CFLAGS=""
user_LDFLAGS="$LDFLAGS"
-AC_ARG_ENABLE(intel64, [ --enable-intel64 optimize for Intel64 CPU such as Xeon and Core2],
- [ext_CFLAGS="${ext_CFLAGS} -mtune=nocona"], [])
-
AC_ARG_ENABLE([debug],
[AS_HELP_STRING([--enable-debug],
[enable debugging info (default is no)])],
[], [enable_debug=no])
-AC_ARG_ENABLE([optim],
- [AS_HELP_STRING([--enable-optim@<:@=0|1|2|3@:>@],
- [set optimization level (default is 3)])],
- [if test "x$enable_optim" = xyes; then enable_optim=3; fi],
- [enable_optim=3])
-AS_IF([test "x$enable_optim" != xno], [ext_CFLAGS="$ext_CFLAGS -O$enable_optim"])
AS_IF([test "x$enable_debug" = xyes],
[debug_CFLAGS="-DDEBUG"],
[debug_CFLAGS="-DNDEBUG"])
CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
CXXFLAGS="$CFLAGS"
-CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2"
+CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS"
LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS"
AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])
@@ -122,7 +102,7 @@
-- ${PACKAGE_STRING} Configuration Results --
C++ compiler: ${CXX} ${CXXFLAGS}
Linker flags: ${LDFLAGS}
- BOOST libraries: ${BOOST_THREAD_LIBS}"
+ BOOST libraries: ${BOOST_THREAD_LIB}"
if test x"${GCC}" = x"yes" ; then
gcc_version=`${CC} --version | head -n 1`
--- a/src/Makefile.am
+++ b/src/Makefile.am
@@ -683,17 +683,12 @@
SeqAn-1.4.2/seqan/system/system_thread.h \
SeqAn-1.4.2/seqan/version.h
-SAMDIR = ./samtools-0.1.18
-SAMLIB = libbam.a
-SAMPROG = samtools_0.1.18
-BAM_LIB = -lbam
-BAM_CPPFLAGS = -I$(SAMDIR)
-BAM_LDFLAGS = -L$(SAMDIR)
+BAM_LIB = -lbam-0.1-legacy
+AM_CPPFLAGS = -I/usr/include/bam-0.1-legacy/
#-- progs to be installed in $prefix/bin
bin_PROGRAMS = \
- $(SAMPROG) \
prep_reads \
gtf_to_fasta \
fix_map_ordering \
@@ -722,9 +717,6 @@
tophat2 \
tophat
-clean-local:
- cd $(SAMDIR) && make clean
-
tophat2: tophat2.sh
cp tophat2.sh tophat2 && chmod 755 tophat2
@@ -732,7 +724,7 @@
sed -e 's|__VERSION__|$(VERSION)|' tophat.py > tophat && chmod 755 tophat
#-- tophat library for linking convienence
-noinst_LIBRARIES = $(SAMLIB) libgc.a libtophat.a
+noinst_LIBRARIES = libgc.a libtophat.a
noinst_HEADERS = \
reads.h \
@@ -801,11 +793,11 @@
prep_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
segment_juncs_SOURCES = segment_juncs.cpp
-segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+segment_juncs_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
segment_juncs_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
long_spanning_reads_SOURCES = long_spanning_reads.cpp
-long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+long_spanning_reads_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
long_spanning_reads_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
gtf_juncs_SOURCES = gtf_juncs.cpp
@@ -817,7 +809,7 @@
juncs_db_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
tophat_reports_SOURCES = tophat_reports.cpp
-tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIBS) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
+tophat_reports_LDADD = $(top_builddir)/src/libtophat.a $(BOOST_THREAD_LIB) $(BOOST_SYSTEM_LIB) $(BAM_LIB)
tophat_reports_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS) $(BOOST_LDFLAGS)
fix_map_ordering_SOURCES = fix_map_ordering.cpp
@@ -844,15 +836,5 @@
gtf_to_fasta_LDADD = $(top_builddir)/src/libtophat.a libgc.a $(BAM_LIB)
gtf_to_fasta_LDFLAGS = $(BAM_LDFLAGS) $(LDFLAGS)
-
-libbam_a_SOURCES =
-samtools_0_1_18_SOURCES =
-
-$(SAMPROG): $(SAMLIB)
-
-
-$(SAMLIB):
- cd $(SAMDIR) && make $(SAMPROG) && cp $(SAMLIB) $(SAMPROG) ..
-
install-data-hook:
cp -r intervaltree sortedcontainers $(DESTDIR)$(bindir)

8
sci-biology/tophat/metadata.xml
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@@ -1,8 +0,0 @@
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
<maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
</pkgmetadata>

83
sci-biology/tophat/tophat-2.1.1-r5.ebuild
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@@ -1,83 +0,0 @@
# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
PYTHON_COMPAT=( python2_7 )
inherit autotools eutils flag-o-matic python-single-r1 toolchain-funcs
DESCRIPTION="Python-based splice junction mapper for RNA-Seq reads using bowtie2"
HOMEPAGE="https://ccb.jhu.edu/software/tophat/"
SRC_URI="https://ccb.jhu.edu/software/tophat/downloads/${P}.tar.gz"
LICENSE="Artistic"
SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="debug"
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
RDEPEND="${PYTHON_DEPS}
dev-libs/boost:=[threads]
$(python_gen_cond_dep '
dev-python/intervaltree[${PYTHON_MULTI_USEDEP}]
dev-python/sortedcontainers[${PYTHON_MULTI_USEDEP}]
')
sci-biology/samtools:0.1-legacy
sci-biology/bowtie:2"
DEPEND="${RDEPEND}
virtual/pkgconfig
sci-biology/seqan:1.4
>=sys-devel/autoconf-archive-2016.09.16"
PATCHES=(
"${FILESDIR}"/${P}-unbundle-seqan-samtools.patch
"${FILESDIR}"/${P}-fix-c++14.patch
"${FILESDIR}"/${P}-python2-shebangs.patch
)
src_prepare() {
default
# remove bundled libs
rm -rf src/samtools-0.1.18/ src/SeqAn-1.4.2/ || die
sed -e "s:samtools_0.1.18:${EPREFIX}/usr/bin/samtools-0.1-legacy/samtools:" \
-i src/tophat.py src/common.cpp || die
sed -e "s:/usr/include/bam-0.1-legacy/:${EPREFIX}/usr/include/bam-0.1-legacy/:" \
-e '/^samtools-0\.1\.18\//d' \
-e '/^SeqAn-1\.4\.2\//d' \
-e 's:sortedcontainers/sortedset.py \\:sortedcontainers/sortedset.py:' \
-e 's:\$(top_builddir)\/src\/::' \
-i src/Makefile.am || die
sed -e 's:\$(top_builddir)\/src\/::' -i src/Makefile.am || die
# innocuous non-security flags, prevent log pollution
append-cflags -Wno-unused-but-set-variable -Wno-unused-variable
append-cppflags "$($(tc-getPKG_CONFIG) --cflags seqan-1.4)"
# remove ancient autoconf archive macros, wreaking havoc,
# depend on sys-devel/autoconf-archive instead, bug #594810
rm {ax_boost_thread,ax_boost_base}.m4 || die
eautoreconf
}
src_configure() {
econf $(use_enable debug)
}
src_install() {
default
# delete bundled python modules
local i
for i in intervaltree sortedcontainers; do
rm -r "${ED%/}"/usr/bin/${i} || die
done
}
pkg_postinst() {
optfeature "ABI SOLiD colorspace reads" sci-biology/bowtie:1
}