commit: f101e36b3fa1e6d87707d5695371c14af5d365e3
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 08:51:56 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 08:52:13 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f101e36b
sci-biology/SPAdes: version bump 3.15.0, fix fetching, add keyword
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
profiles/package.mask | 1 -
sci-biology/SPAdes/SPAdes-3.13.0.ebuild | 74 ----------------------
.../{SPAdes-3.14.1.ebuild => SPAdes-3.15.0.ebuild} | 31 +++------
3 files changed, 8 insertions(+), 98 deletions(-)
diff --git a/profiles/package.mask b/profiles/package.mask
index 640ce0789..076004dee 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -104,4 +104,3 @@ sci-biology/skewer-bin
sci-biology/smalt
sci-biology/SnpEff
sci-biology/snphylo
-sci-biology/SPAdes
diff --git a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
deleted file mode 100644
index d3c1e0a57..000000000
--- a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
+++ /dev/null
@@ -1,74 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# 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
-
-DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
-HOMEPAGE="http://cab.spbu.ru/software/spades";
-SRC_URI="
- 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}/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 ->
${P}_dipspades_manual.html"
-# DEPRECATED in 3.12.0: dipSPAdes pipeline for highly polymorphic diploid
genomes
-# (still present in the release but no longer supported)
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
- sys-libs/zlib
- app-arch/bzip2
- dev-python/regex"
-RDEPEND="${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 || $(gcc-major-version) -lt 4 ]] ; then
- eerror "You need at least sys-devel/gcc-4.7.0"
- die "You need at least sys-devel/gcc-4.7.0"
- fi
- fi
- fi
-}
-
-src_compile(){
- PREFIX="${ED}"/usr ./spades_compile.sh || die
-}
-
-src_install(){
- # BUG: move *.py files to standard site-packages/ subdirectories
- insinto /usr/share/"${PN}"
- dodoc "${DISTDIR}"/${P}_*manual.html
-}
diff --git a/sci-biology/SPAdes/SPAdes-3.14.1.ebuild
b/sci-biology/SPAdes/SPAdes-3.15.0.ebuild
similarity index 58%
rename from sci-biology/SPAdes/SPAdes-3.14.1.ebuild
rename to sci-biology/SPAdes/SPAdes-3.15.0.ebuild
index 773ccf658..3e8943607 100644
--- a/sci-biology/SPAdes/SPAdes-3.14.1.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.15.0.ebuild
@@ -1,29 +1,25 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
-
-PYTHON_COMPAT=( python{2_7,3_{4,5}} )
-
-inherit eutils toolchain-funcs
+EAPI=7
DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
-HOMEPAGE="http://cab.spbu.ru/software/spades";
+HOMEPAGE="https://cab.spbu.ru/software/spades";
SRC_URI="
https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
- http://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
- http://cab.spbu.ru/files/release${PV}/rnaspades_manual.html ->
${P}_rnaspades_manual.html
- http://cab.spbu.ru/files/release${PV}/truspades_manual.html ->
${P}_truspades_manual.html"
+ https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html
+ https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html ->
${P}_rnaspades_manual.html
+ https://cab.spbu.ru/files/release${PV}/truspades_manual.html ->
${P}_truspades_manual.html"
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS=""
-IUSE=""
+KEYWORDS="~amd64"
DEPEND="
sys-libs/zlib
app-arch/bzip2
dev-python/regex"
RDEPEND="${DEPEND}"
+BDEPEND="dev-util/cmake"
# BUG:
# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are
used,
# not *.so or *.a are even used)
@@ -48,17 +44,6 @@ RDEPEND="${DEPEND}"
# 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 || $(gcc-major-version) -lt 4 ]] ; then
- eerror "You need at least sys-devel/gcc-4.7.0"
- die "You need at least sys-devel/gcc-4.7.0"
- fi
- fi
- fi
-}
-
src_compile(){
PREFIX="${ED}"/usr ./spades_compile.sh || die
}
