* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2017-01-29 18:08 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2017-01-29 18:08 UTC (permalink / raw
To: gentoo-commits
commit: 8ef2d0632281aeb653b62b10b8da00f22f9cc62d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan 29 18:08:40 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jan 29 18:08:40 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8ef2d063
sci-biology/SPAdes: version bump, remove old, src_install actually does also src_compile
Upstream contacted to split compile and install steps into separate procedures.
The Gentoo package should be probably renamed to all lowercase letters.
Hierarchy in /usr/share/spades/ is a bit awkward.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
.../{SPAdes-3.5.0.ebuild => SPAdes-3.9.1.ebuild} | 23 +++++++++++-----------
sci-biology/SPAdes/metadata.xml | 7 ++++++-
2 files changed, 17 insertions(+), 13 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild b/sci-biology/SPAdes/SPAdes-3.9.1.ebuild
similarity index 64%
rename from sci-biology/SPAdes/SPAdes-3.5.0.ebuild
rename to sci-biology/SPAdes/SPAdes-3.9.1.ebuild
index 45cb010..1a5a5d5 100644
--- a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.9.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -11,8 +11,8 @@ inherit eutils toolchain-funcs
DESCRIPTION="De novo de Bruijn genome assembler (bacteria to fungi) or uneven coverage"
HOMEPAGE="http://bioinf.spbau.ru/en/spades"
SRC_URI="
- http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz
- http://spades.bioinf.spbau.ru/release3.5.0/manual.html"
+ http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz
+ http://spades.bioinf.spbau.ru/release${PV}/manual.html -> ${P}_manual.html"
LICENSE="GPL-2"
SLOT="0"
@@ -37,14 +37,13 @@ pkg_pretend() {
fi
}
-src_prepare(){
- insinto /usr/share/doc/SPAdes
- dodoc "${DISTDIR}"/manual.html
-}
+#src_compile(){
+# # grr, it actually also installs the files into $DESTDIR but that is purged before pkg_qmerge starts
+# PREFIX="${D}"/usr ./spades_compile.sh || die
+#}
-src_compile(){
- # grr, it actually also installs the files into $PREFIX
- PREFIX="${D}"/usr ./spades_compile.sh || die
+src_install(){
+ PREFIX="${ED}"/usr ./spades_compile.sh || die
+ insinto /usr/share/"${PN}"
+ dodoc "${DISTDIR}"/manual.html
}
-
-# BUG: contents of "${D}" do not propagate during qmerge?
diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml
index 1699e58..4baa308 100644
--- a/sci-biology/SPAdes/metadata.xml
+++ b/sci-biology/SPAdes/metadata.xml
@@ -5,8 +5,13 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
-<maintainer type="project">
+ <maintainer type="project">
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <longdescription>
+ truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
+ hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
+ dipspades is assembly module for highly polymorphic diploid genomes
+ </longdescription>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2024-01-22 19:29 Horea Christian
0 siblings, 0 replies; 23+ messages in thread
From: Horea Christian @ 2024-01-22 19:29 UTC (permalink / raw
To: gentoo-commits
commit: 0ad60f57bec0408d59349751ced4f5c7f22a3b72
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 22 19:29:16 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 22 19:29:16 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0ad60f57
sci-biology/SPAdes: added comment for next release
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/SPAdes/SPAdes-3.15.5.ebuild | 2 ++
1 file changed, 2 insertions(+)
diff --git a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
index 4485619e3..026dd0476 100644
--- a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
@@ -29,6 +29,8 @@ DEPEND="
RDEPEND="${DEPEND}"
BDEPEND="dev-build/cmake"
+# Remove for next release:
+# https://github.com/ablab/spades/issues/1238#issuecomment-1904427831
PATCHES=(
"${FILESDIR}/${P}-gcc13.patch"
)
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2024-01-22 19:28 Horea Christian
0 siblings, 0 replies; 23+ messages in thread
From: Horea Christian @ 2024-01-22 19:28 UTC (permalink / raw
To: gentoo-commits
commit: a9b2100efac435eb6fc2140c1a906d0a2758984a
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 22 19:28:18 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 22 19:28:18 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a9b2100e
sci-biology/SPAdes: drop 3.15.3
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/SPAdes/SPAdes-3.15.3.ebuild | 38 ---------------------------------
1 file changed, 38 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
deleted file mode 100644
index b6d344c37..000000000
--- a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
+++ /dev/null
@@ -1,38 +0,0 @@
-# Copyright 1999-2022 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..12} )
-inherit python-single-r1
-
-DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
-HOMEPAGE="https://cab.spbu.ru/software/spades"
-SRC_URI="
- https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
- https://cab.spbu.ru/files/release${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 -> ${P}_truspades_manual.html
-"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-# Fails to build:
-# https://github.com/ablab/spades/issues/1238
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-DEPEND="
- sys-libs/zlib
- app-arch/bzip2
- dev-python/regex
- ${PYTHON_DEPS}
-"
-RDEPEND="${DEPEND}"
-BDEPEND="dev-build/cmake"
-
-src_install(){
- einstalldocs
- # WORKAROUND: This script does both compile and install in one go
- PREFIX="${ED}"/usr ./spades_compile.sh || die
-}
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2024-01-22 13:01 Horea Christian
0 siblings, 0 replies; 23+ messages in thread
From: Horea Christian @ 2024-01-22 13:01 UTC (permalink / raw
To: gentoo-commits
commit: 8cd68194088f5c91057700f1f0def5fe733e9e19
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 22 13:00:48 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 22 13:00:48 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8cd68194
sci-biology/SPAdes: unkeyword 3.15.3 for ~amd64
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/SPAdes/SPAdes-3.15.3.ebuild | 4 +++-
1 file changed, 3 insertions(+), 1 deletion(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
index 4f01f669f..b6d344c37 100644
--- a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
@@ -17,7 +17,9 @@ SRC_URI="
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
+# Fails to build:
+# https://github.com/ablab/spades/issues/1238
REQUIRED_USE="${PYTHON_REQUIRED_USE}"
DEPEND="
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2024-01-22 13:01 Horea Christian
0 siblings, 0 replies; 23+ messages in thread
From: Horea Christian @ 2024-01-22 13:01 UTC (permalink / raw
To: gentoo-commits
commit: aea1a69a5dae783cccfe1d3f513e5d090188a279
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 22 13:01:18 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 22 13:01:18 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=aea1a69a
sci-biology/SPAdes: add 3.15.5
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/SPAdes/SPAdes-3.15.5.ebuild | 38 +++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)
diff --git a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
new file mode 100644
index 000000000..b6d344c37
--- /dev/null
+++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+inherit python-single-r1
+
+DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
+HOMEPAGE="https://cab.spbu.ru/software/spades"
+SRC_URI="
+ https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
+ 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 -> ${P}_truspades_manual.html
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+# Fails to build:
+# https://github.com/ablab/spades/issues/1238
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="
+ sys-libs/zlib
+ app-arch/bzip2
+ dev-python/regex
+ ${PYTHON_DEPS}
+"
+RDEPEND="${DEPEND}"
+BDEPEND="dev-build/cmake"
+
+src_install(){
+ einstalldocs
+ # WORKAROUND: This script does both compile and install in one go
+ PREFIX="${ED}"/usr ./spades_compile.sh || die
+}
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2024-01-22 13:01 Horea Christian
0 siblings, 0 replies; 23+ messages in thread
From: Horea Christian @ 2024-01-22 13:01 UTC (permalink / raw
To: gentoo-commits
commit: f40f597ed62ebbcece98ba6ec2569f8aa09dc654
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 22 12:55:04 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 22 12:55:04 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f40f597e
sci-biology/SPAdes: enable py3.11, py3.12
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/SPAdes/SPAdes-3.15.3.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
index 7c404dfd0..4f01f669f 100644
--- a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
@@ -3,7 +3,7 @@
EAPI=8
-PYTHON_COMPAT=( python3_10 )
+PYTHON_COMPAT=( python3_{10..12} )
inherit python-single-r1
DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2024-01-22 13:01 Horea Christian
0 siblings, 0 replies; 23+ messages in thread
From: Horea Christian @ 2024-01-22 13:01 UTC (permalink / raw
To: gentoo-commits
commit: 54e72942b81551d47a0ebc0b1893181e1082613c
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 22 12:57:51 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 22 12:57:51 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=54e72942
sci-biology/SPAdes: add github upstream metadata
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/SPAdes/metadata.xml | 11 +++++++----
1 file changed, 7 insertions(+), 4 deletions(-)
diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml
index 0845ad7a4..5f573393e 100644
--- a/sci-biology/SPAdes/metadata.xml
+++ b/sci-biology/SPAdes/metadata.xml
@@ -10,8 +10,11 @@
<name>Gentoo Biology Project</name>
</maintainer>
<longdescription>
-truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
-hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
-dipspades is assembly module for highly polymorphic diploid genomes
-</longdescription>
+ truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads.
+ hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp.
+ dipspades is assembly module for highly polymorphic diploid genomes
+ </longdescription>
+ <upstream>
+ <remote-id type="github">ablab/spades</remote-id>
+ </upstream>
</pkgmetadata>
^ permalink raw reply related [flat|nested] 23+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2024-01-22 13:01 Horea Christian
0 siblings, 0 replies; 23+ messages in thread
From: Horea Christian @ 2024-01-22 13:01 UTC (permalink / raw
To: gentoo-commits
commit: 57e58b916ee04062b4683b6dc2178f1ad0d1c348
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Mon Jan 22 12:32:54 2024 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Mon Jan 22 12:32:54 2024 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=57e58b91
sci-biology/SPAdes: updated cmake dependency category
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/SPAdes/SPAdes-3.15.3.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
index 002004bca..7c404dfd0 100644
--- a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
@@ -27,7 +27,7 @@ DEPEND="
${PYTHON_DEPS}
"
RDEPEND="${DEPEND}"
-BDEPEND="dev-util/cmake"
+BDEPEND="dev-build/cmake"
src_install(){
einstalldocs
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2022-01-25 14:24 Andrew Ammerlaan
0 siblings, 0 replies; 23+ messages in thread
From: Andrew Ammerlaan @ 2022-01-25 14:24 UTC (permalink / raw
To: gentoo-commits
commit: 34773140d758b76b35f70f857f7b27ee06503921
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue Jan 25 14:24:18 2022 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue Jan 25 14:24:18 2022 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=34773140
sci-biology/SPAdes: bump to 3.15.3
Package-Manager: Portage-3.0.30, Repoman-3.0.3
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/SPAdes/SPAdes-3.15.1.ebuild | 55 ---------------------------------
sci-biology/SPAdes/SPAdes-3.15.3.ebuild | 36 +++++++++++++++++++++
2 files changed, 36 insertions(+), 55 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
deleted file mode 100644
index 853524984..000000000
--- a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
-HOMEPAGE="https://cab.spbu.ru/software/spades"
-SRC_URI="
- https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
- 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 -> ${P}_truspades_manual.html"
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="
- sys-libs/zlib
- app-arch/bzip2
- dev-python/regex"
-RDEPEND="${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)
-#
-# 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
-
-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-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
new file mode 100644
index 000000000..553c21e21
--- /dev/null
+++ b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+inherit python-single-r1
+
+DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
+HOMEPAGE="https://cab.spbu.ru/software/spades"
+SRC_URI="
+ https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz
+ 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 -> ${P}_truspades_manual.html
+"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+REQUIRED_USE="${PYTHON_REQUIRED_USE}"
+
+DEPEND="
+ sys-libs/zlib
+ app-arch/bzip2
+ dev-python/regex
+ ${PYTHON_DEPS}
+"
+RDEPEND="${DEPEND}"
+BDEPEND="dev-util/cmake"
+
+src_install(){
+ einstalldocs
+ # WORKAROUND: This script does both compile and install in one go
+ PREFIX="${ED}"/usr ./spades_compile.sh || die
+}
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2021-03-05 13:34 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2021-03-05 13:34 UTC (permalink / raw
To: gentoo-commits
commit: 257e4e9f1776f2fe2e5e5a348a2f15f7baeec1ad
Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Fri Mar 5 13:34:24 2021 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 5 13:34:24 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=257e4e9f
sci-biology/SPAdes: dropping KEYWORDS
src_install() phase does not install the files
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>
sci-biology/SPAdes/SPAdes-3.15.1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
index 3e8943607..853524984 100644
--- a/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
@@ -12,7 +12,7 @@ SRC_URI="
https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html"
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
DEPEND="
sys-libs/zlib
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2021-03-05 9:22 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2021-03-05 9:22 UTC (permalink / raw
To: gentoo-commits
commit: 11e7e6552d00645d27360186f403c23dfc807099
Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Fri Mar 5 09:21:36 2021 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Mar 5 09:21:36 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=11e7e655
sci-biology/SPAdes: version bump to 3.15.1
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>
sci-biology/SPAdes/{SPAdes-3.15.0.ebuild => SPAdes-3.15.1.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.15.0.ebuild b/sci-biology/SPAdes/SPAdes-3.15.1.ebuild
similarity index 100%
rename from sci-biology/SPAdes/SPAdes-3.15.0.ebuild
rename to sci-biology/SPAdes/SPAdes-3.15.1.ebuild
^ permalink raw reply [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2020-05-15 19:31 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2020-05-15 19:31 UTC (permalink / raw
To: gentoo-commits
commit: f3a538b68e80b3fc42af81717f48a5cbfb283f45
Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com>
AuthorDate: Fri May 15 19:30:28 2020 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri May 15 19:30:47 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f3a538b6
sci-biology/SPAdes: version bump to 3.14.1
This is a bug-fix release, which includes:
- Fix for read filtering tool;
- Soft and hard-filtered transcripts are now copied to the output
folder in rnaSPAdes;
- Minor fix in biosyntheticSPAdes pipeline;
- Minor fix in metaplasmidSPAdes contig output;
- Several usability fixes in `spades.py';
- Other minor bug-fixes.
Package-Manager: Portage-2.3.99, Repoman-2.3.22
Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com>
sci-biology/SPAdes/{SPAdes-3.14.0.ebuild => SPAdes-3.14.1.ebuild} | 6 +-----
1 file changed, 1 insertion(+), 5 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.14.0.ebuild b/sci-biology/SPAdes/SPAdes-3.14.1.ebuild
similarity index 87%
rename from sci-biology/SPAdes/SPAdes-3.14.0.ebuild
rename to sci-biology/SPAdes/SPAdes-3.14.1.ebuild
index d3c1e0a57..773ccf658 100644
--- a/sci-biology/SPAdes/SPAdes-3.14.0.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.14.1.ebuild
@@ -13,11 +13,7 @@ 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 -> ${P}_dipspades_manual.html"
-# DEPRECATED in 3.12.0: dipSPAdes pipeline for highly polymorphic diploid genomes
-# (still present in the release but no longer supported)
-
+ http://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS=""
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2020-01-06 17:14 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2020-01-06 17:14 UTC (permalink / raw
To: gentoo-commits
commit: 84bb511d7a904b2e151faa1f9224dd91a196349f
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Jan 6 17:13:56 2020 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Jan 6 17:13:56 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=84bb511d
sci-biology/SPAdes: version bump
- BiosyntheticSPAdes pipeline for identifying Biosynthetic Gene Clusters (BGCs)
- Hybrid transcriptome assembly (Illumina RNA-Seq + Iso-seq / ONT RNA)
- Plasmid assembly from metagenomic datasets
- New --isolate option that improves assembly quality of standard datasets with
high coverage
- New standalone tools for read filtration based on k-mer coverage and
estimating number of unique k-mers in reads
- Improved SPAligner tool for read-to-graph alignment
- Major performance improvements and memory consumption reduction in graph
construction, simplification procedures and throughout the whole pipeline
- Several bug-fixes.
Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>
sci-biology/SPAdes/SPAdes-3.13.0.ebuild | 2 +-
sci-biology/SPAdes/{SPAdes-3.13.0.ebuild => SPAdes-3.14.0.ebuild} | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
index 00ccc4f27..d3c1e0a57 100644
--- a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
diff --git a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild b/sci-biology/SPAdes/SPAdes-3.14.0.ebuild
similarity index 98%
copy from sci-biology/SPAdes/SPAdes-3.13.0.ebuild
copy to sci-biology/SPAdes/SPAdes-3.14.0.ebuild
index 00ccc4f27..d3c1e0a57 100644
--- a/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.14.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2018-10-16 17:47 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2018-10-16 17:47 UTC (permalink / raw
To: gentoo-commits
commit: f7eaea4317cca5c6ca5566c05c69b604d7312bc8
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Oct 16 17:47:08 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Oct 16 17:47:08 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f7eaea43
sci-biology/SPAdes: version bump, drop old and buggy version
SPAdes 3.13.0
CHANGE: Switched to multi-k-mer mode in rnaSPAdes, k-mer values are detected
automatically based on read length.
CHANGE: Added manual as README.md in markdown format for github.
FIX: Updated BWA and switched to RopeBWT, which allows to handle large graphs.
FIX: Assert for path.length() > 0 in rnaSPAdes.
FIX: CQF and k-mer counting.
REMOVE: dipSPAdes module.
Package-Manager: Portage-2.3.51, Repoman-2.3.10
sci-biology/SPAdes/{SPAdes-3.12.0.ebuild => SPAdes-3.13.0.ebuild} | 1 -
1 file changed, 1 deletion(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.12.0.ebuild b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
similarity index 96%
rename from sci-biology/SPAdes/SPAdes-3.12.0.ebuild
rename to sci-biology/SPAdes/SPAdes-3.13.0.ebuild
index b56180a1a..00ccc4f27 100644
--- a/sci-biology/SPAdes/SPAdes-3.12.0.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.13.0.ebuild
@@ -12,7 +12,6 @@ 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}/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 -> ${P}_dipspades_manual.html"
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2018-01-09 22:03 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2018-01-09 22:03 UTC (permalink / raw
To: gentoo-commits
commit: 4dd7fc5f1806465684c1101c88021ab3e1993fa2
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jan 9 22:03:02 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jan 9 22:03:02 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4dd7fc5f
sci-biology/SPAdes: version bump
Try to follow the upstream's approach to compile and install
the tool. src_compile() therefore does also src_install()
into a DESTDIR.
Package-Manager: Portage-2.3.19, Repoman-2.3.6
sci-biology/SPAdes/SPAdes-3.11.1.ebuild | 72 +++++++++++++++++++++++++++++++++
1 file changed, 72 insertions(+)
diff --git a/sci-biology/SPAdes/SPAdes-3.11.1.ebuild b/sci-biology/SPAdes/SPAdes-3.11.1.ebuild
new file mode 100644
index 000000000..1842fca37
--- /dev/null
+++ b/sci-biology/SPAdes/SPAdes-3.11.1.ebuild
@@ -0,0 +1,72 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python{2_7,3_{4,5}} )
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
+HOMEPAGE="http://cab.spbu.ru/software/spades"
+SRC_URI="
+ http://spades.bioinf.spbau.ru/release${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 || $(gcc-major-version) -lt 4 ]] ; then
+ eerror "You need at least sys-devel/gcc-4.7.0"
+ die "You need at least sys-devel/gcc-4.7.0"
+ fi
+ fi
+ fi
+}
+
+src_compile(){
+ PREFIX="${ED}"/usr ./spades_compile.sh || die
+}
+
+src_install(){
+ # BUG: move *.py files to standard site-packages/ subdirectories
+ insinto /usr/share/"${PN}"
+ dodoc "${DISTDIR}"/${P}_*manual.html
+}
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2017-07-28 20:05 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2017-07-28 20:05 UTC (permalink / raw
To: gentoo-commits
commit: c9670fe28445edf107eb51db383a7833e65056f4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Jul 28 19:13:58 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Jul 28 20:05:19 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c9670fe2
sci-biology/SPAdes: update comments on bundled dev-libs/boost
Package-Manager: Portage-2.3.6, Repoman-2.3.3
sci-biology/SPAdes/SPAdes-3.10.1.ebuild | 3 ++-
1 file changed, 2 insertions(+), 1 deletion(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
index a887fe909..3d219dbf0 100644
--- a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
@@ -27,7 +27,8 @@ DEPEND="
dev-python/regex"
RDEPEND="${DEPEND}"
# BUG:
-# SPAdes uses bundled while modified copy of dev-libs/boost
+# SPAdes uses bundled while modified copy of dev-libs/boost (only headers are used,
+# not *.so or *.a are even used)
#
# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their
# existing packages
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2017-05-14 18:48 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2017-05-14 18:48 UTC (permalink / raw
To: gentoo-commits
commit: 4036ac0a6d0616ae423c7de5f5f6dfc60bd83e6f
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun May 14 18:48:46 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun May 14 18:48:46 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4036ac0a
sci-biology/SPAdes: drop DEPENDency on boost
Upstream says SPAdes uses bundled while modified local copy.
Fix URL to new official site.
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/SPAdes/SPAdes-3.10.1.ebuild | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
index de93157a4..a887fe909 100644
--- a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
@@ -5,10 +5,10 @@ EAPI=6
PYTHON_COMPAT=( python{2_7,3_{4,5}} )
-inherit eutils toolchain-funcs
+inherit eutils toolchain-funcs cmake-utils
DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
-HOMEPAGE="http://bioinf.spbau.ru/en/spades"
+HOMEPAGE="http://cab.spbu.ru/software/spades"
SRC_URI="
http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz
http://spades.bioinf.spbau.ru/release${PV}/manual.html -> ${P}_manual.html
@@ -24,10 +24,11 @@ IUSE=""
DEPEND="
sys-libs/zlib
app-arch/bzip2
- dev-python/regex
- dev-libs/boost"
+ dev-python/regex"
RDEPEND="${DEPEND}"
-
+# BUG:
+# SPAdes uses bundled while modified copy of dev-libs/boost
+#
# BUG: "${S}"/ext/src/ contains plenty of bundled 3rd-party tools. Drop them all and properly DEPEND on their
# existing packages
# nlopt
@@ -44,7 +45,7 @@ RDEPEND="${DEPEND}"
# samtools
# bwa
-# BUG: "${S}"/ext/tools/ contains even two version of bwa
+# BUG: "${S}"/ext/tools/ contains even two version of bwa, being installed as bwa-spades binary?
# bwa-0.7.12
# bwa-0.6.2
@@ -76,6 +77,7 @@ src_compile(){
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
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2017-05-14 11:49 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2017-05-14 11:49 UTC (permalink / raw
To: gentoo-commits
commit: 7a4c5e17a64afe18b4af992e6b2df279ecd9e7e6
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun May 14 11:49:02 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun May 14 11:49:02 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7a4c5e17
sci-biology/SPAdes: install the package directly using cmake
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/SPAdes/SPAdes-3.10.1.ebuild | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
index 73050c1e4..de93157a4 100644
--- a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
@@ -68,12 +68,14 @@ src_prepare(){
}
src_compile(){
- # grr, it actually also installs the files into $DESTDIR but that is purged before pkg_qmerge starts
- PREFIX="${D}"/usr ./spades_compile.sh || die
+ mkdir build_spades || die
+ cd build_spades || die
+ cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="${ED}/usr" $* "${S}/src" || die
}
src_install(){
- PREFIX="${ED}"/usr sh ./spades_install.sh || die
+ cd build_spades || die
+ emake install PREFIX="${ED}"/usr
# BUG: move *.py files to standard site-packages/ subdirectories
insinto /usr/share/"${PN}"
dodoc "${DISTDIR}"/${P}_*manual.html
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2017-05-13 15:08 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2017-05-13 15:08 UTC (permalink / raw
To: gentoo-commits
commit: c3b614f81dae512b5798b74c2d9cd46952507f5c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May 13 15:08:08 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May 13 15:08:08 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c3b614f8
sci-biology/SPAdes: improve DESCRIPTION
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/SPAdes/SPAdes-3.10.1.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
index 6a21643a8..36f724d83 100644
--- a/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
@@ -7,7 +7,7 @@ PYTHON_COMPAT=( python{2_7,3_{4,5}} )
inherit eutils toolchain-funcs
-DESCRIPTION="De novo de Bruijn genome assembler (bacteria to fungi) or uneven coverage"
+DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage"
HOMEPAGE="http://bioinf.spbau.ru/en/spades"
SRC_URI="
http://spades.bioinf.spbau.ru/release${PV}/SPAdes-${PV}.tar.gz
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2017-05-12 18:10 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2017-05-12 18:10 UTC (permalink / raw
To: gentoo-commits
commit: e1a1e06331c449e29b30cf97df54d2f4d7b69de7
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri May 12 18:10:06 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri May 12 18:10:06 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e1a1e063
sci-biology/SPAdes: version bump
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/SPAdes/{SPAdes-3.9.1.ebuild => SPAdes-3.10.1.ebuild} | 0
1 file changed, 0 insertions(+), 0 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.9.1.ebuild b/sci-biology/SPAdes/SPAdes-3.10.1.ebuild
similarity index 100%
rename from sci-biology/SPAdes/SPAdes-3.9.1.ebuild
rename to sci-biology/SPAdes/SPAdes-3.10.1.ebuild
^ permalink raw reply [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2017-01-29 18:13 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2017-01-29 18:13 UTC (permalink / raw
To: gentoo-commits
commit: 8d6ea3fcf39703a49e09ad80d65f25988d54c17a
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan 29 18:13:23 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jan 29 18:13:23 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8d6ea3fc
sci-biology/SPAdes: install more HTML documentation
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/SPAdes/SPAdes-3.9.1.ebuild | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.9.1.ebuild b/sci-biology/SPAdes/SPAdes-3.9.1.ebuild
index 1a5a5d5..5c8b66f 100644
--- a/sci-biology/SPAdes/SPAdes-3.9.1.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.9.1.ebuild
@@ -12,7 +12,10 @@ DESCRIPTION="De novo de Bruijn genome assembler (bacteria to fungi) or uneven co
HOMEPAGE="http://bioinf.spbau.ru/en/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}/manual.html -> ${P}_manual.html
+ http://spades.bioinf.spbau.ru/release3.9.1/dipspades_manual.html -> ${P}_dipspades_manual.html
+ http://spades.bioinf.spbau.ru/release3.9.1/rnaspades_manual.html -> ${P}_rnaspades_manual.html
+ http://spades.bioinf.spbau.ru/release3.9.1/truspades_manual.html -> ${P}_truspades_manual.html"
LICENSE="GPL-2"
SLOT="0"
@@ -45,5 +48,5 @@ pkg_pretend() {
src_install(){
PREFIX="${ED}"/usr ./spades_compile.sh || die
insinto /usr/share/"${PN}"
- dodoc "${DISTDIR}"/manual.html
+ dodoc "${DISTDIR}"/${P}_*manual.html
}
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2016-04-08 20:07 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2016-04-08 20:07 UTC (permalink / raw
To: gentoo-commits
commit: 0d4a3b17f010a8f80e089f4ea1c6f0eef9cb3eb0
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 8 20:04:32 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 8 20:04:32 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0d4a3b17
sci-biology/SPAdes: improve description
Package-Manager: portage-2.2.28
sci-biology/SPAdes/SPAdes-3.5.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild b/sci-biology/SPAdes/SPAdes-3.5.0.ebuild
index 4cc246b..f9a6ee9 100644
--- a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild
+++ b/sci-biology/SPAdes/SPAdes-3.5.0.ebuild
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} )
inherit eutils toolchain-funcs
-DESCRIPTION="De novo assembler for smaller genomes (bacteria to fungi)"
+DESCRIPTION="De novo de Bruijn genome assembler (bacteria to fungi) or uneven coverage"
HOMEPAGE="http://bioinf.spbau.ru/en/spades"
SRC_URI="http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz
http://spades.bioinf.spbau.ru/release3.5.0/manual.html"
^ permalink raw reply related [flat|nested] 23+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/SPAdes/
@ 2016-02-10 15:22 Martin Mokrejs
0 siblings, 0 replies; 23+ messages in thread
From: Martin Mokrejs @ 2016-02-10 15:22 UTC (permalink / raw
To: gentoo-commits
commit: 413c2c2dd02a27666281094f516976c8c7f3f357
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Feb 10 15:20:19 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Feb 10 15:20:19 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=413c2c2d
sci-biology/SPAdes: new package
Package-Manager: portage-2.2.26
sci-biology/SPAdes/SPAdes-3.5.0.ebuild | 48 ++++++++++++++++++++++++++++++++++
sci-biology/SPAdes/metadata.xml | 9 +++++++
2 files changed, 57 insertions(+)
diff --git a/sci-biology/SPAdes/SPAdes-3.5.0.ebuild b/sci-biology/SPAdes/SPAdes-3.5.0.ebuild
new file mode 100644
index 0000000..7265909
--- /dev/null
+++ b/sci-biology/SPAdes/SPAdes-3.5.0.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_7,3_2,3_3,3_4} )
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="De novo assembler for smaller genomes (bacteria to fungi)"
+HOMEPAGE="http://bioinf.spbau.ru/en/spades"
+SRC_URI="http://spades.bioinf.spbau.ru/release3.5.0/SPAdes-3.5.0.tar.gz
+ http://spades.bioinf.spbau.ru/release3.5.0/manual.html"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="sys-libs/zlib
+ app-arch/bzip2
+ dev-python/regex
+ dev-libs/boost"
+RDEPEND="${DEPEND}"
+
+pkg_pretend() {
+ if [[ ${MERGE_TYPE} != binary ]]; then
+ if [[ $(tc-getCXX) == *g++ ]] ; then
+ if [[ $(gcc-major-version) == 4 && $(gcc-minor-version) -lt 7 || $(gcc-major-version) -lt 4 ]] ; then
+ eerror "You need at least sys-devel/gcc-4.7.0"
+ die "You need at least sys-devel/gcc-4.7.0"
+ fi
+ fi
+ fi
+}
+
+src_prepare(){
+ insinto /usr/share/doc/SPAdes
+ dodoc "${DISTDIR}"/manual.html
+}
+
+src_compile(){
+ # grr, it actually also installs the files into $PREFIX
+ PREFIX="${D}"/usr ./spades_compile.sh || die
+}
+
+# BUG: contents of "${D}" do not propagate during qmerge?
diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/SPAdes/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 23+ messages in thread
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