[gentoo-commits] proj/sci:master commit in: sci-biology/amos/, sci-biology/amos/files/

[Benda XU]

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>mmokrejs@×××××××××××××××.cz</email>
-		<name>Martin Mokrejs</name>
-	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@g.o</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>