commit: c22df03ee45b3384f0c929d4c1349de89d6f3153 Author: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> AuthorDate: Fri Feb 28 07:30:13 2020 +0000 Commit: Mikle Kolyada <zlogene <AT> gentoo <DOT> org> CommitDate: Fri Feb 28 07:30:13 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=c22df03e
sci-biology/tophat: remove last-rited package Signed-off-by: Mikle Kolyada <zlogene <AT> gentoo.org> sci-biology/tophat/Manifest | 1 - .../tophat/files/tophat-2.1.1-fix-c++14.patch | 14 -- .../files/tophat-2.1.1-python2-shebangs.patch | 42 ------ .../tophat-2.1.1-unbundle-seqan-samtools.patch | 162 --------------------- sci-biology/tophat/metadata.xml | 8 - sci-biology/tophat/tophat-2.1.1-r5.ebuild | 83 ----------- 6 files changed, 310 deletions(-) diff --git a/sci-biology/tophat/Manifest b/sci-biology/tophat/Manifest deleted file mode 100644 index 05897bbf09e..00000000000 --- a/sci-biology/tophat/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST tophat-2.1.1.tar.gz 2259554 BLAKE2B f01b08cc2046b7d143864d64aa3e34d3000c7c10d7e50a4e102d500556e8620996de03392463f9d08ae97858eaec85b2df3b5d5ee5b0b4f7a5c0ae06bb3d08e8 SHA512 e2e0943a6f3d34b83922e6e403b65a3bee480a2b2bb4bf2de0cae7e0ef5bb166b66fec923316c2b643e8550e43c842f0f1bcc2ca7249d20fbcf5a4733fbdeabc diff --git a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch b/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch deleted file mode 100644 index e8168bb9143..00000000000 --- a/sci-biology/tophat/files/tophat-2.1.1-fix-c++14.patch +++ /dev/null @@ -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()); diff --git a/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch b/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch deleted file mode 100644 index 5c38bcc072e..00000000000 --- a/sci-biology/tophat/files/tophat-2.1.1-python2-shebangs.patch +++ /dev/null @@ -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 - """ diff --git a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch b/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch deleted file mode 100644 index 9d0a2694051..00000000000 --- a/sci-biology/tophat/files/tophat-2.1.1-unbundle-seqan-samtools.patch +++ /dev/null @@ -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) diff --git a/sci-biology/tophat/metadata.xml b/sci-biology/tophat/metadata.xml deleted file mode 100644 index 959160fe46b..00000000000 --- a/sci-biology/tophat/metadata.xml +++ /dev/null @@ -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-biol...@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/tophat/tophat-2.1.1-r5.ebuild b/sci-biology/tophat/tophat-2.1.1-r5.ebuild deleted file mode 100644 index 75318877138..00000000000 --- a/sci-biology/tophat/tophat-2.1.1-r5.ebuild +++ /dev/null @@ -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 -}
