* [gentoo-commits] proj/sci:master commit in: sci-biology/quast/
@ 2014-03-23 16:48 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2014-03-23 16:48 UTC (permalink / raw
To: gentoo-commits
commit: ba8d30305983c8aec216c07d62218879a12793c9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 16:46:42 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 16:46:42 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ba8d3030
sci-biology/quast: a skeleton for a new python-based package, need help
Package-Manager: portage-2.2.7
---
sci-biology/quast/ChangeLog | 9 +++++++++
sci-biology/quast/metadata.xml | 9 +++++++++
sci-biology/quast/quast-2.2.ebuild | 35 +++++++++++++++++++++++++++++++++++
3 files changed, 53 insertions(+)
diff --git a/sci-biology/quast/ChangeLog b/sci-biology/quast/ChangeLog
new file mode 100644
index 0000000..578e834
--- /dev/null
+++ b/sci-biology/quast/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/quast
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*quast-2.2 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+ +quast-2.2.ebuild:
+ sci-biology/quast: a skeleton for a new python-based package, need help
diff --git a/sci-biology/quast/metadata.xml b/sci-biology/quast/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/quast/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>
diff --git a/sci-biology/quast/quast-2.2.ebuild b/sci-biology/quast/quast-2.2.ebuild
new file mode 100644
index 0000000..5f6c9b9
--- /dev/null
+++ b/sci-biology/quast/quast-2.2.ebuild
@@ -0,0 +1,35 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit python
+
+DESCRIPTION="Compare quality of multiple genome assemblies to each other"
+HOMEPAGE="http://bioinf.spbau.ru/QUAST"
+SRC_URI="http://sourceforge.net/projects/quast/files/"$P".tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-python/matplotlib
+ sci-biology/mummer
+ sci-biology/glimmerhmm"
+# sci-biology/GAGE
+# sci-biology/GeneMarkS
+# sci-biology/MetaGeneMark"
+
+# the above packages need to be created first
+
+RDEPEND="${DEPEND}
+ dev-lang/perl"
+
+src_install(){
+ dobin quast.py metaquast.py
+ dodoc manual.html CHANGES
+
+ # TODO: install lib/ subdirectory contents into some PATH and PYTHON_PATH
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/quast/
@ 2014-11-13 13:00 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2014-11-13 13:00 UTC (permalink / raw
To: gentoo-commits
commit: 2f57a1458981371ddbaeec83168e30b231075c6b
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Thu Nov 13 12:37:44 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Thu Nov 13 12:37:44 2014 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2f57a145
sci-biology/quast: Bump to new python eclasses
Package-Manager: portage-2.2.14
---
sci-biology/quast/ChangeLog | 3 +++
sci-biology/quast/metadata.xml | 10 +++++-----
sci-biology/quast/quast-2.2.ebuild | 26 +++++++++++++++-----------
3 files changed, 23 insertions(+), 16 deletions(-)
diff --git a/sci-biology/quast/ChangeLog b/sci-biology/quast/ChangeLog
index 578e834..ccf3a0e 100644
--- a/sci-biology/quast/ChangeLog
+++ b/sci-biology/quast/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 13 Nov 2014; Justin Lecher <jlec@gentoo.org> quast-2.2.ebuild, metadata.xml:
+ Bump to new python eclasses
+
*quast-2.2 (23 Mar 2014)
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
diff --git a/sci-biology/quast/metadata.xml b/sci-biology/quast/metadata.xml
index 07b5255..2bc8930 100644
--- a/sci-biology/quast/metadata.xml
+++ b/sci-biology/quast/metadata.xml
@@ -1,9 +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>
+ <herd>sci-biology</herd>
+ <maintainer>
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
</pkgmetadata>
diff --git a/sci-biology/quast/quast-2.2.ebuild b/sci-biology/quast/quast-2.2.ebuild
index 5f6c9b9..3839147 100644
--- a/sci-biology/quast/quast-2.2.ebuild
+++ b/sci-biology/quast/quast-2.2.ebuild
@@ -4,31 +4,35 @@
EAPI=5
-inherit python
+PYTHON_COMPAT=( python2_7 )
+
+inherit python-r1
DESCRIPTION="Compare quality of multiple genome assemblies to each other"
HOMEPAGE="http://bioinf.spbau.ru/QUAST"
-SRC_URI="http://sourceforge.net/projects/quast/files/"$P".tar.gz"
+SRC_URI="http://sourceforge.net/projects/quast/files/${P}.tar.gz"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS=""
IUSE=""
-DEPEND="dev-python/matplotlib
- sci-biology/mummer
- sci-biology/glimmerhmm"
-# sci-biology/GAGE
-# sci-biology/GeneMarkS
-# sci-biology/MetaGeneMark"
+DEPEND="
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ sci-biology/mummer
+ sci-biology/glimmerhmm"
+# sci-biology/GAGE
+# sci-biology/GeneMarkS
+# sci-biology/MetaGeneMark"
# the above packages need to be created first
-RDEPEND="${DEPEND}
- dev-lang/perl"
+RDEPEND="${DEPEND}"
src_install(){
- dobin quast.py metaquast.py
+ python_foreach_impl python_newscript quast.py quast
+ python_foreach_impl python_newscript metaquast.py metaquast
+
dodoc manual.html CHANGES
# TODO: install lib/ subdirectory contents into some PATH and PYTHON_PATH
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/quast/
@ 2015-01-15 11:49 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-01-15 11:49 UTC (permalink / raw
To: gentoo-commits
commit: c0b00572f627ef5eefae26c0c8630b9cef580639
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 15 11:48:05 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 15 11:48:05 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c0b00572
version bump
Package-Manager: portage-2.2.7
---
sci-biology/quast/ChangeLog | 8 +++++++-
sci-biology/quast/{quast-2.2.ebuild => quast-2.3.ebuild} | 2 +-
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/quast/ChangeLog b/sci-biology/quast/ChangeLog
index ccf3a0e..ed58021 100644
--- a/sci-biology/quast/ChangeLog
+++ b/sci-biology/quast/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-biology/quast
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*quast-2.3 (15 Jan 2015)
+
+ 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +quast-2.3.ebuild,
+ -quast-2.2.ebuild:
+ version bump
+
13 Nov 2014; Justin Lecher <jlec@gentoo.org> quast-2.2.ebuild, metadata.xml:
Bump to new python eclasses
diff --git a/sci-biology/quast/quast-2.2.ebuild b/sci-biology/quast/quast-2.3.ebuild
similarity index 95%
rename from sci-biology/quast/quast-2.2.ebuild
rename to sci-biology/quast/quast-2.3.ebuild
index 3839147..3cf92e3 100644
--- a/sci-biology/quast/quast-2.2.ebuild
+++ b/sci-biology/quast/quast-2.3.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2015 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/quast/
@ 2015-01-15 11:52 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-01-15 11:52 UTC (permalink / raw
To: gentoo-commits
commit: 2bdf22d7d9d5d8553287cf6c324a69a2e4a3226e
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 15 11:51:33 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 15 11:51:33 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2bdf22d7
added a note about additional bundled package licenses
Package-Manager: portage-2.2.7
---
sci-biology/quast/ChangeLog | 3 +++
sci-biology/quast/quast-2.3.ebuild | 2 +-
2 files changed, 4 insertions(+), 1 deletion(-)
diff --git a/sci-biology/quast/ChangeLog b/sci-biology/quast/ChangeLog
index ed58021..e29320d 100644
--- a/sci-biology/quast/ChangeLog
+++ b/sci-biology/quast/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> quast-2.3.ebuild:
+ added a note about additional bundled package licenses
+
*quast-2.3 (15 Jan 2015)
15 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +quast-2.3.ebuild,
diff --git a/sci-biology/quast/quast-2.3.ebuild b/sci-biology/quast/quast-2.3.ebuild
index 3cf92e3..701f274 100644
--- a/sci-biology/quast/quast-2.3.ebuild
+++ b/sci-biology/quast/quast-2.3.ebuild
@@ -12,7 +12,7 @@ DESCRIPTION="Compare quality of multiple genome assemblies to each other"
HOMEPAGE="http://bioinf.spbau.ru/QUAST"
SRC_URI="http://sourceforge.net/projects/quast/files/${P}.tar.gz"
-LICENSE="GPL-2"
+LICENSE="GPL-2" # and some other for the bundled copies, see http://quast.bioinf.spbau.ru/LICENSE
SLOT="0"
KEYWORDS=""
IUSE=""
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/quast/
@ 2017-01-29 18:29 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2017-01-29 18:29 UTC (permalink / raw
To: gentoo-commits
commit: 8d68b0e9000600e9cfce3d6cee7b4779929f3840
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan 29 18:29:24 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jan 29 18:29:24 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8d68b0e9
sci-biology/quast: updating to a current version, still incomplete
This will need much more work to unbundle all the required stuff.
Package-Manager: Portage-2.3.3, Repoman-2.3.1
sci-biology/quast/{quast-2.3.ebuild => quast-4.4.ebuild} | 14 ++++++++++----
1 file changed, 10 insertions(+), 4 deletions(-)
diff --git a/sci-biology/quast/quast-2.3.ebuild b/sci-biology/quast/quast-4.4.ebuild
similarity index 67%
rename from sci-biology/quast/quast-2.3.ebuild
rename to sci-biology/quast/quast-4.4.ebuild
index cc33280..3e992ba 100644
--- a/sci-biology/quast/quast-2.3.ebuild
+++ b/sci-biology/quast/quast-4.4.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
@@ -23,7 +23,11 @@ DEPEND="
sci-biology/glimmerhmm"
# sci-biology/GAGE
# sci-biology/GeneMarkS
-# sci-biology/MetaGeneMark"
+# sci-biology/GeneMarkES
+# sci-biology/MetaGeneMark
+# sci-biology/ncbi-tools++
+#
+# comes with bundled executables in ./quast_libs
# the above packages need to be created first
@@ -32,8 +36,10 @@ RDEPEND="${DEPEND}"
src_install(){
python_foreach_impl python_newscript quast.py quast
python_foreach_impl python_newscript metaquast.py metaquast
+ python_foreach_impl python_newscript icarus.py icarus
- dodoc manual.html CHANGES
+ dodoc manual.html
- # TODO: install lib/ subdirectory contents into some PATH and PYTHON_PATH
+ # TODO: install quast_libs/ subdirectory contents into some PATH and PYTHON_PATH
+ # TODO: unbundle bundled executables
}
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/quast/
@ 2021-01-05 6:08 Horea Christian
0 siblings, 0 replies; 7+ messages in thread
From: Horea Christian @ 2021-01-05 6:08 UTC (permalink / raw
To: gentoo-commits
commit: 18a06b432038370bfdb59f2ab8b043d7874ccfce
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 4 15:37:42 2021 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Jan 5 06:08:00 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=18a06b43
sci-biology/quast: version bump, add keywords, bump py targets
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/quast/quast-4.4.ebuild | 44 ------------------------------------
sci-biology/quast/quast-5.0.2.ebuild | 23 +++++++++++++++++++
2 files changed, 23 insertions(+), 44 deletions(-)
diff --git a/sci-biology/quast/quast-4.4.ebuild b/sci-biology/quast/quast-4.4.ebuild
deleted file mode 100644
index 7ac6905c3..000000000
--- a/sci-biology/quast/quast-4.4.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit python-r1
-
-DESCRIPTION="Compare quality of multiple genome assemblies to each other"
-HOMEPAGE="http://bioinf.spbau.ru/QUAST" # no https
-SRC_URI="https://sourceforge.net/projects/quast/files/${P}.tar.gz"
-
-LICENSE="GPL-2" # and some other for the bundled copies, see http://quast.bioinf.spbau.ru/LICENSE
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
- dev-python/matplotlib[${PYTHON_USEDEP}]
- sci-biology/mummer
- sci-biology/glimmerhmm"
-# sci-biology/GAGE
-# sci-biology/GeneMarkS
-# sci-biology/GeneMarkES
-# sci-biology/MetaGeneMark
-# sci-biology/ncbi-tools++
-#
-# comes with bundled executables in ./quast_libs
-
-# the above packages need to be created first
-
-RDEPEND="${DEPEND}"
-
-src_install(){
- python_foreach_impl python_newscript quast.py quast
- python_foreach_impl python_newscript metaquast.py metaquast
- python_foreach_impl python_newscript icarus.py icarus
-
- dodoc manual.html
-
- # TODO: install quast_libs/ subdirectory contents into some PATH and PYTHON_PATH
- # TODO: unbundle bundled executables
-}
diff --git a/sci-biology/quast/quast-5.0.2.ebuild b/sci-biology/quast/quast-5.0.2.ebuild
new file mode 100644
index 000000000..eb49a803b
--- /dev/null
+++ b/sci-biology/quast/quast-5.0.2.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Compare quality of multiple genome assemblies to each other"
+HOMEPAGE="http://bioinf.spbau.ru/QUAST" # no https
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-python/joblib[${PYTHON_USEDEP}]
+ dev-python/simplejson[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests --install setup.py
^ permalink raw reply related [flat|nested] 7+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/quast/
@ 2023-05-02 12:15 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:15 UTC (permalink / raw
To: gentoo-commits
commit: e60a848577cff478a2d846b202129cfacd9a4537
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May 2 12:11:02 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May 2 12:15:18 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e60a8485
sci-biology/quast: treeclean
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/quast/metadata.xml | 15 ---------------
sci-biology/quast/quast-5.0.2.ebuild | 23 -----------------------
2 files changed, 38 deletions(-)
diff --git a/sci-biology/quast/metadata.xml b/sci-biology/quast/metadata.xml
deleted file mode 100644
index c821b722e..000000000
--- a/sci-biology/quast/metadata.xml
+++ /dev/null
@@ -1,15 +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@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="sourceforge">quast</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/quast/quast-5.0.2.ebuild b/sci-biology/quast/quast-5.0.2.ebuild
deleted file mode 100644
index eb49a803b..000000000
--- a/sci-biology/quast/quast-5.0.2.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Compare quality of multiple genome assemblies to each other"
-HOMEPAGE="http://bioinf.spbau.ru/QUAST" # no https
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
- dev-python/joblib[${PYTHON_USEDEP}]
- dev-python/simplejson[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests --install setup.py
^ permalink raw reply related [flat|nested] 7+ messages in thread
end of thread, other threads:[~2023-05-02 12:15 UTC | newest]
Thread overview: 7+ messages (download: mbox.gz follow: Atom feed
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