commit: 5ef25a48bee2090fbcd6a9e92d4a8299c88edc67
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu May 17 19:37:29 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu May 17 19:37:29 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=5ef25a48
sci-biology/SPAdes: version bump, drop old
Package-Manager: Portage-2.3.36, Repoman-2.3.9
sci-biology/SPAdes/SPAdes-3.10.1.ebuild | 85 ----------------------
.../{SPAdes-3.11.1.ebuild => SPAdes-3.12.0.ebuild} | 13 ++--
.../files/SPAdes-3.10.1-fix-missing-include.patch | 10 ---
3 files changed, 8 insertions(+), 100 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
deleted file mode 100644
index 3d219dbf0..000000000
--- a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
+++ /dev/null
@@ -1,85 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_{4,5}} )
-
-inherit eutils toolchain-funcs cmake-utils
-
-DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
-HOMEPAGE="http://cab.spbu.ru/software/spades";
-SRC_URI="
- http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz
- http://spades.bioinf.spbau.ru/release${PV}/manual.html ->
${P}_manual.html
- http://spades.bioinf.spbau.ru/release${PV}/dipspades_manual.html ->
${P}_dipspades_manual.html
- http://spades.bioinf.spbau.ru/release${PV}/rnaspades_manual.html ->
${P}_rnaspades_manual.html
- http://spades.bioinf.spbau.ru/release${PV}/truspades_manual.html ->
${P}_truspades_manual.html"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
- sys-libs/zlib
- app-arch/bzip2
- dev-python/regex"
-RDEPEND="${DEPEND}"
-# BUG:
-# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are
used,
-# not *.so or *.a are even used)
-#
-# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them
all and properly DEPEND on their
-# existing packages
-# nlopt
-# llvm
-# python_libs
-# bamtools
-# ConsensusCore
-# ssw
-# jemalloc
-# htrie
-# getopt_pp
-# cppformat
-# cityhash
-# samtools
-# bwa
-
-# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as
bwa-spades binary?
-# bwa-0.7.12
-# bwa-0.6.2
-
-pkg_pretend() {
- if [[ ${MERGE_TYPE} != binary ]]; then
- if [[ $(tc-getCXX) == *g++ ]] ; then
- if [[ $(gcc-major-version) == 4 && $(gcc-minor-version)
-lt 7 || $(gcc-major-version) -lt 4 ]] ; then
- eerror "You need at least sys-devel/gcc-4.7.0"
- die "You need at least sys-devel/gcc-4.7.0"
- fi
- fi
- fi
-}
-
-src_prepare(){
- # https://github.com/Homebrew/homebrew-science/pull/5616
- epatch "${FILESDIR}"/"${P}"-fix-missing-include.patch
- cp -p spades_compile.sh spades_install.sh || die
- sed -e 's/make install/#make install/;s/cd $PREFIX/#cd $PREFIX/' -i
spades_compile.sh || die
- default
-}
-
-src_compile(){
- mkdir build_spades || die
- cd build_spades || die
- cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="${ED}/usr" $*
"${S}/src" || die
-}
-
-src_install(){
- cd build_spades || die
- emake install PREFIX="${ED}"/usr
- # cmake-utils_src_install # dies with "${S}" does not appear to contain
CMakeLists.txt
- # BUG: move *.py files to standard site-packages/ subdirectories
- insinto /usr/share/"${PN}"
- dodoc "${DISTDIR}"/${P}_*manual.html
-}
diff --git a/sci-biology/SPAdes/SPAdes-3.11.1.ebuild
b/sci-biology/SPAdes/SPAdes-3.12.0.ebuild
similarity index 70%
rename from sci-biology/SPAdes/SPAdes-3.11.1.ebuild
rename to sci-biology/SPAdes/SPAdes-3.12.0.ebuild
index 1842fca37..b56180a1a 100644
--- a/sci-biology/SPAdes/SPAdes-3.11.1.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.12.0.ebuild
@@ -10,11 +10,14 @@ inherit eutils toolchain-funcs
DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
HOMEPAGE="http://cab.spbu.ru/software/spades";
SRC_URI="
- http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz
- http://spades.bioinf.spbau.ru/release${PV}/manual.html ->
${P}_manual.html
- http://spades.bioinf.spbau.ru/release${PV}/dipspades_manual.html ->
${P}_dipspades_manual.html
- http://spades.bioinf.spbau.ru/release${PV}/rnaspades_manual.html ->
${P}_rnaspades_manual.html
- http://spades.bioinf.spbau.ru/release${PV}/truspades_manual.html ->
${P}_truspades_manual.html"
+ https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
+ http://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
+ http://cab.spbu.ru/files/release${PV}/manual.md -> ${P}_manual.md
+ http://cab.spbu.ru/files/release${PV}/rnaspades_manual.html ->
${P}_rnaspades_manual.html
+ http://cab.spbu.ru/files/release${PV}/truspades_manual.html ->
${P}_truspades_manual.html
+ http://spades.bioinf.spbau.ru/release3.11.1/dipspades_manual.html ->
${P}_dipspades_manual.html"
+# DEPRECATED in 3.12.0: dipSPAdes pipeline for highly polymorphic diploid
genomes
+# (still present in the release but no longer supported)
LICENSE="GPL-2"
SLOT="0"
diff --git a/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch
b/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch
deleted file mode 100644
index bb6d75797..000000000
--- a/sci-biology/SPAdes/files/SPAdes-3.10.1-fix-missing-include.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- SPAdes-3.10.1/src/common/utils/segfault_handler.hpp.ori 2017-05-13
22:43:01.296207276 +0200
-+++ SPAdes-3.10.1/src/common/utils/segfault_handler.hpp 2017-05-13
22:43:41.437310225 +0200
-@@ -12,6 +12,7 @@
- #include "boost/noncopyable.hpp"
-
- #include <signal.h>
-+#include <functional>
-
- struct segfault_handler : boost::noncopyable {
- typedef std::function<void()> callback_t;
