commit: 435cdfbb48bf8efd38cb3198230758bd599aeac3 Author: Benda Xu <heroxbd <AT> gentoo <DOT> org> AuthorDate: Mon Feb 3 03:22:24 2020 +0000 Commit: Benda XU <heroxbd <AT> gentoo <DOT> org> CommitDate: Mon Feb 3 04:02:34 2020 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=435cdfbb
sci-biology/amos: remove from tree. 1. No upstream development since 2011. 2. Does not support Python 3. Bug: https://bugs.gentoo.org/707558 Signed-off-by: Benda Xu <heroxbd <AT> gentoo.org> sci-biology/amos/amos-3.1.0-r2.ebuild | 76 ---------------------- sci-biology/amos/amos-9999.ebuild | 76 ---------------------- sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch | 15 ----- ...mos-3.1.0-goBambus2.py-indent-and-cleanup.patch | 25 ------- .../files/amos-3.1.0-rename_to_jellyfish1.patch | 43 ------------ .../amos/files/amos-9999-fix-include-paths.patch | 13 ---- sci-biology/amos/metadata.xml | 21 ------ 7 files changed, 269 deletions(-) diff --git a/sci-biology/amos/amos-3.1.0-r2.ebuild b/sci-biology/amos/amos-3.1.0-r2.ebuild deleted file mode 100644 index 951f12c1b..000000000 --- a/sci-biology/amos/amos-3.1.0-r2.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) -inherit eutils python-r1 - -PERL_EXPORT_PHASE_FUNCTIONS=no -inherit perl-module eutils toolchain-funcs - -DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies" -HOMEPAGE="http://amos.sourceforge.net/"; -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="mpi qt5" - -DEPEND=" - mpi? ( virtual/mpi ) - dev-libs/boost - qt5? ( dev-qt/qtcore:5 ) - sci-biology/blat - sci-biology/jellyfish:1" -RDEPEND="${DEPEND} - dev-lang/perl - dev-perl/DBI - dev-perl/Statistics-Descriptive - sci-biology/mummer" - -MAKEOPTS+=" -j1" - -src_prepare() { - epatch \ - "${FILESDIR}"/${P}-gcc-4.7.patch \ - "${FILESDIR}"/${P}-goBambus2.py-indent-and-cleanup.patch \ - "${FILESDIR}"/${P}-rename_to_jellyfish1.patch - # $ gap-links - # ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/ - # $ - sh ./bootstrap || die - default - eautoreconf - # prevent GCC 6 log pollution due to hash_map deprecation in C++11 - # shutdown gcc-8.2.0 messages too - append-cxxflags -Wno-cpp -Wno-narrowing -} - -src_configure() { - local myconf - use X && myconf+=( --with-x ) - econf ${myconf[@]} --with-jellyfish="${EPREFIX}"/usr/include --with-Boost-dir="${EPREFIX}"/usr/include --with-qmake-qt4=qmake --enable-all -} - -src_install() { - default - python_replicate_script "${ED}"/usr/bin/goBambus2 - # bambus needs TIGR::FASTAreader.pm and others - # configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it - perl_set_version - insinto ${VENDOR_LIB}/AMOS - doins "${D}"/usr/lib64/AMOS/*.pm - insinto ${VENDOR_LIB}/TIGR - doins "${D}"/usr/lib64/TIGR/*.pm - # move also /usr/lib64/AMOS/AMOS.py to /usr/bin - mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die - # zap the mis-placed files ('make install' is at fault) - rm -f "${D}"/usr/lib64/AMOS/*.pm - rm -rf "${D}"/usr/lib64/TIGR - echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die - mkdir -p "${ED}"/etc || die - touch "${ED}"/etc/amos.acf || die - doenvd "${S}/99amos" -} diff --git a/sci-biology/amos/amos-9999.ebuild b/sci-biology/amos/amos-9999.ebuild deleted file mode 100644 index 923ac5978..000000000 --- a/sci-biology/amos/amos-9999.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -PYTHON_COMPAT=( python2_7 ) - -PERL_EXPORT_PHASE_FUNCTIONS=no -inherit perl-module eutils toolchain-funcs autotools flag-o-matic python-single-r1 qmake-utils - -AUTOTOOLS_AUTORECONF=true -inherit autotools-utils git-r3 - -DESCRIPTION="Whole genome assembler, Hawkeye and AMOScmp to compare multiple assemblies" -HOMEPAGE="http://sourceforge.net/projects/amos"; -SRC_URI="" -EGIT_REPO_URI="git://amos.git.sourceforge.net/gitroot/amos/amos" - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="" -IUSE="mpi qt5 X" - -DEPEND=" - mpi? ( virtual/mpi ) - dev-libs/boost - qt5? ( dev-qt/qtcore:5 ) - sci-biology/blat - sci-biology/jellyfish:1" -RDEPEND="${DEPEND} - dev-perl/DBI - dev-perl/Statistics-Descriptive - sci-biology/mummer" - -# $ gap-links -# ERROR: Could not open file LIBGUESTFS_PATH=/usr/share/guestfs/appliance/ -# $ - -src_prepare() { - epatch "${FILESDIR}"/"${P}"-fix-include-paths.patch - epatch "${FILESDIR}"/amos-3.1.0-rename_to_jellyfish1.patch - sh ./bootstrap || die - default - eautoreconf - - # prevent GCC 6 log pollution due to hash_map deprecation in C++11 - # shutdown gcc-8.2.0 messages too - append-cxxflags -Wno-cpp -Wno-narrowing -} - -src_configure() { - local myconf - use X && myconf+=( --with-x ) - econf ${myconf[@]} --with-jellyfish="${EPREFIX}"/usr/include --with-Boost-dir="${EPREFIX}"/usr/include --with-qmake-qt4=qmake --enable-all -} - -src_install() { - default - python_replicate_script "${ED}"/usr/bin/goBambus2 - # bambus needs TIGR::FASTAreader.pm and others - # configure --libdir sadly copies both *.a files and *.pm into /usr/lib64/AMOS/ and /usr/lib64/TIGR/, work around it - perl_set_version - insinto ${VENDOR_LIB}/AMOS - doins "${D}"/usr/lib64/AMOS/*.pm - insinto ${VENDOR_LIB}/TIGR - doins "${D}"/usr/lib64/TIGR/*.pm - # move also /usr/lib64/AMOS/AMOS.py to /usr/bin - mv "${D}"/usr/lib64/AMOS/*.py "${D}"/usr/bin || die - # zap the mis-placed files ('make install' is at fault) - rm -f "${D}"/usr/lib64/AMOS/*.pm - rm -rf "${D}"/usr/lib64/TIGR - echo AMOSCONF="${EPREFIX}"/etc/amos.acf > "${S}"/99amos || die - mkdir -p "${ED}"/etc || die - touch "${ED}"/etc/amos.acf || die - doenvd "${S}/99amos" -} diff --git a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch b/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch deleted file mode 100644 index de2a41184..000000000 --- a/sci-biology/amos/files/amos-3.1.0-gcc-4.7.patch +++ /dev/null @@ -1,15 +0,0 @@ - src/Align/find-tandem.cc | 1 + - 1 files changed, 1 insertions(+), 0 deletions(-) - -diff --git a/src/Align/find-tandem.cc b/src/Align/find-tandem.cc -index ddf1cab..a29e21e 100644 ---- a/src/Align/find-tandem.cc -+++ b/src/Align/find-tandem.cc -@@ -7,6 +7,7 @@ - #include <vector> - #include <ctime> - #include <sys/time.h> -+#include <unistd.h> - using namespace std; - - const int OFFSET_TABLE_SIZE = 100; diff --git a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch b/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch deleted file mode 100644 index 97a8f59d0..000000000 --- a/sci-biology/amos/files/amos-3.1.0-goBambus2.py-indent-and-cleanup.patch +++ /dev/null @@ -1,25 +0,0 @@ ---- amos-3.1.0/src/Pipeline/goBambus2.py.orig 2013-09-11 01:05:29.850090457 +0200 -+++ amos-3.1.0/src/Pipeline/goBambus2.py 2013-09-11 01:07:03.250090701 +0200 -@@ -1,7 +1,7 @@ - #pipeline script for assembly + Bambus 2 - #contributed by Todd J Treangen - --import string, sys, os, subprocess#, spincursor -+import sys, os, subprocess#, spincursor - - RED = "\033[0;31m" - GREEN = "\033[0;32m" -@@ -360,7 +360,7 @@ - print "\t\t%s...failed%s"%(RED,NONE) - sys.exit(1) - -- p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) -+ p = subprocess.Popen(AMOSDIR+"OutputResults -b %s -prefix %s %s"%(amosbank, prefix+".scaff.linear"), shell=True, stdin=subprocess.PIPE, stdout=vtext, stderr=logfile) - - if xopt_dict["verbose"] == 1: - print "10) running OutputResults" -@@ -388,4 +388,3 @@ - else: - print "\t\t%s...failed%s"%(RED,NONE) - sys.exit(1) --) diff --git a/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch b/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch deleted file mode 100644 index 4b52c5640..000000000 --- a/sci-biology/amos/files/amos-3.1.0-rename_to_jellyfish1.patch +++ /dev/null @@ -1,43 +0,0 @@ ---- config/amos.m4 2018-09-11 13:23:14.478444129 +0200 -+++ config/amos.m4 2018-09-11 13:36:36.697612245 +0200 -@@ -695,15 +695,15 @@ - else - jellyfish_unspecified=no - fi --if ! test -f "$jellyfish_dir/jellyfish/mer_counting.hpp"; then -+if ! test -f "$jellyfish_dir/jellyfish1/mer_counting.hpp"; then - if test $jellyfish_unspecified = no; then -- AC_MSG_ERROR([Could not find the file "$jellyfish_dir/jellyfish/compacted_hash.hpp"]) -+ AC_MSG_ERROR([Could not find the file "$jellyfish_dir/jellyfish1/compacted_hash.hpp"]) - fi - JELLYFISH_LDADD= - JELLYFISH_CPPFLAGS= - AC_MSG_RESULT([not found]) - else -- JELLYFISH_LDADD="-ljellyfish -lpthread" -+ JELLYFISH_LDADD="-ljellyfish-1.1 -lpthread" - JELLYFISH_CPPFLAGS="-I $jellyfish_dir" - AC_DEFINE([WITH_JELLYFISH], [1], [Define to 1 if using Jellyfish]) - cppflags_save="$CPPFLAGS" -@@ -715,7 +715,7 @@ - AC_LANG_PUSH([C++]) - AC_LINK_IFELSE([ - AC_LANG_PROGRAM([ --#include <jellyfish/mer_counting.hpp> -+#include <jellyfish1/mer_counting.hpp> - #include <string> - ], [ - std::string s; ---- src/Align/kmer-cov-plot.cc 2018-09-11 13:23:15.079443556 +0200 -+++ src/Align/kmer-cov-plot.cc 2018-09-11 13:36:36.831612096 +0200 -@@ -388,8 +388,8 @@ - - #ifdef WITH_JELLYFISH - --#include <jellyfish/compacted_hash.hpp> --#include <jellyfish/mer_counting.hpp> -+#include <jellyfish1/compacted_hash.hpp> -+#include <jellyfish1/mer_counting.hpp> - - // Assert that jellyfish is using the expected kmer representation - static void jellyfish_check() diff --git a/sci-biology/amos/files/amos-9999-fix-include-paths.patch b/sci-biology/amos/files/amos-9999-fix-include-paths.patch deleted file mode 100644 index a6e8dc9f0..000000000 --- a/sci-biology/amos/files/amos-9999-fix-include-paths.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- src/Bambus/Bundler/Makefile.am.old 2018-07-03 12:52:17.306095693 +0200 -+++ src/Bambus/Bundler/Makefile.am 2018-07-03 12:52:19.506101530 +0200 -@@ -78,8 +78,8 @@ - ##-- libBundler.a - libBundler_a_CPPFLAGS = \ - $(BOOST_CXXFLAGS) \ -- -I$(top_builddir)/src/GNU \ -- -I$(top_builddir)/src/AMOS -+ -I$(top_srcdir)/src/GNU \ -+ -I$(top_srcdir)/src/AMOS - ## because some system headers will be built if necessary - libBundler_a_LIBADD = \ - $(LIBOBJS:%=$(top_builddir)/src/GNU/%) \ diff --git a/sci-biology/amos/metadata.xml b/sci-biology/amos/metadata.xml deleted file mode 100644 index ddba4784f..000000000 --- a/sci-biology/amos/metadata.xml +++ /dev/null @@ -1,21 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="person"> - <email>[email protected]</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> -AMOS is collection of tools and class interfaces for the assembly of DNA -sequencing reads. The package includes a robust infrastructure, modular assembly -pipelines, and tools for overlapping, consensus generation, contigging, and -assembly manipulation -</longdescription> - <upstream> - <remote-id type="sourceforge">amos</remote-id> - </upstream> -</pkgmetadata>
