* [gentoo-commits] proj/sci:master commit in: sci-biology/oncotator/
@ 2017-04-20 17:05 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2017-04-20 17:05 UTC (permalink / raw
To: gentoo-commits
commit: 8626e7cf15de4a26857f95608e87afdc5a18f947
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 20 17:05:20 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 20 17:05:20 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8626e7cf
sci-biology/oncotator: new package
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/oncotator/metadata.xml | 12 +++++++++
sci-biology/oncotator/oncotator-1.9.2.0.ebuild | 34 ++++++++++++++++++++++++++
2 files changed, 46 insertions(+)
diff --git a/sci-biology/oncotator/metadata.xml b/sci-biology/oncotator/metadata.xml
new file mode 100644
index 000000000..f68a1b6fa
--- /dev/null
+++ b/sci-biology/oncotator/metadata.xml
@@ -0,0 +1,12 @@
+<?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>
+</pkgmetadata>
diff --git a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
new file mode 100644
index 000000000..aa9b07ba9
--- /dev/null
+++ b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_5 )
+inherit distutils-r1
+
+DESCRIPTION="Annotate genetic variants in VCF"
+HOMEPAGE="https://github.com/broadinstitute/oncotator"
+SRC_URI="https://github.com/broadinstitute/oncotator/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="oncotator"
+SLOT="0"
+KEYWORDS="" # breaks silently during install because of python syntax errors
+IUSE=""
+
+DEPEND="
+ >=sci-biology/pysam-0.9.0
+ >=dev-python/bcbio-gff-0.6.2
+ >=dev-python/pyvcf-0.6.8
+ >=dev-python/pandas-0.18.0
+ >=sci-biology/biopython-1.66
+ >=dev-python/numpy-1.11.0
+ >=dev-python/cython-0.24
+ >=dev-python/shove-0.6.6
+ >=dev-python/sqlalchemy-1.0.12
+ >=dev-python/nose-1.3.7
+ >=dev-python/python-memcached-1.57
+ >=dev-python/natsort-4.0.4
+ >=dev-python/more-itertools-2.2
+ >=dev-python/enum34-1.1.2
+ dev-python/ngslib"
+RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/oncotator/
@ 2017-04-20 17:07 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2017-04-20 17:07 UTC (permalink / raw
To: gentoo-commits
commit: 57b259c58ac4e200456b5253c4b9f722531bc0ab
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 20 17:07:36 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 20 17:07:36 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=57b259c5
sci-biology/oncotator: add RESTRICT="fetch" due to issue #362
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/oncotator/oncotator-1.9.2.0.ebuild | 2 ++
1 file changed, 2 insertions(+)
diff --git a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
index aa9b07ba9..cc358c2c2 100644
--- a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
+++ b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
@@ -15,6 +15,8 @@ SLOT="0"
KEYWORDS="" # breaks silently during install because of python syntax errors
IUSE=""
+RESTRICT="fetch"
+
DEPEND="
>=sci-biology/pysam-0.9.0
>=dev-python/bcbio-gff-0.6.2
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/oncotator/
@ 2017-04-20 17:17 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2017-04-20 17:17 UTC (permalink / raw
To: gentoo-commits
commit: 4d527ea9def1ecbf56ffb994a359b093133924bf
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 20 17:17:13 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 20 17:17:13 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4d527ea9
sci-biology/oncotator: drop python3_5 until issue #364 is answered
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/oncotator/oncotator-1.9.2.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
index cc358c2c2..9f18d269a 100644
--- a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
+++ b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
@@ -3,7 +3,7 @@
EAPI=6
-PYTHON_COMPAT=( python2_7 python3_5 )
+PYTHON_COMPAT=( python2_7 )
inherit distutils-r1
DESCRIPTION="Annotate genetic variants in VCF"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/oncotator/
@ 2017-04-20 17:22 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2017-04-20 17:22 UTC (permalink / raw
To: gentoo-commits
commit: d68adfb9942a65c7bd497c8d735e50cc010d5154
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 20 17:22:38 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 20 17:22:38 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d68adfb9
sci-biology/oncotator: add LICENSE, add KEYWORDS
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/oncotator/oncotator-1.9.2.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
index 9f18d269a..a8a042d1d 100644
--- a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
+++ b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
@@ -12,7 +12,7 @@ SRC_URI="https://github.com/broadinstitute/oncotator/archive/v${PV}.tar.gz -> ${
LICENSE="oncotator"
SLOT="0"
-KEYWORDS="" # breaks silently during install because of python syntax errors
+KEYWORDS="~amd64 ~x86" # breaks silently during install because of python syntax errors
IUSE=""
RESTRICT="fetch"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/oncotator/
@ 2017-04-30 13:37 Martin Mokrejs
0 siblings, 0 replies; 6+ messages in thread
From: Martin Mokrejs @ 2017-04-30 13:37 UTC (permalink / raw
To: gentoo-commits
commit: c399b73baed076fd9704f7ac3d508eb09ce9c5d4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Apr 30 13:32:28 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Apr 30 13:32:28 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=c399b73b
sci-biology/oncotator: note that python-3.x is not supported
Package-Manager: Portage-2.3.5, Repoman-2.3.2
sci-biology/oncotator/oncotator-1.9.2.0.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
index a8a042d1d..77f439b6d 100644
--- a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
+++ b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
@@ -3,7 +3,7 @@
EAPI=6
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python2_7 ) # no python3+, issue #364
inherit distutils-r1
DESCRIPTION="Annotate genetic variants in VCF"
^ permalink raw reply related [flat|nested] 6+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/oncotator/
@ 2020-09-27 8:09 Horea Christian
0 siblings, 0 replies; 6+ messages in thread
From: Horea Christian @ 2020-09-27 8:09 UTC (permalink / raw
To: gentoo-commits
commit: 4a9c779e4fe5ef995cb4f3a26a4cd0aed1e0789b
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 08:03:36 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 08:03:36 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=4a9c779e
sci-biology/oncotator: rm discontinued package, now part of sci-biology/gatk
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/oncotator/metadata.xml | 15 -----------
sci-biology/oncotator/oncotator-1.9.2.0.ebuild | 36 --------------------------
2 files changed, 51 deletions(-)
diff --git a/sci-biology/oncotator/metadata.xml b/sci-biology/oncotator/metadata.xml
deleted file mode 100644
index 7b9024751..000000000
--- a/sci-biology/oncotator/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="github">broadinstitute/oncotator</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
deleted file mode 100644
index 77f439b6d..000000000
--- a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
+++ /dev/null
@@ -1,36 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 ) # no python3+, issue #364
-inherit distutils-r1
-
-DESCRIPTION="Annotate genetic variants in VCF"
-HOMEPAGE="https://github.com/broadinstitute/oncotator"
-SRC_URI="https://github.com/broadinstitute/oncotator/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="oncotator"
-SLOT="0"
-KEYWORDS="~amd64 ~x86" # breaks silently during install because of python syntax errors
-IUSE=""
-
-RESTRICT="fetch"
-
-DEPEND="
- >=sci-biology/pysam-0.9.0
- >=dev-python/bcbio-gff-0.6.2
- >=dev-python/pyvcf-0.6.8
- >=dev-python/pandas-0.18.0
- >=sci-biology/biopython-1.66
- >=dev-python/numpy-1.11.0
- >=dev-python/cython-0.24
- >=dev-python/shove-0.6.6
- >=dev-python/sqlalchemy-1.0.12
- >=dev-python/nose-1.3.7
- >=dev-python/python-memcached-1.57
- >=dev-python/natsort-4.0.4
- >=dev-python/more-itertools-2.2
- >=dev-python/enum34-1.1.2
- dev-python/ngslib"
-RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 6+ messages in thread
end of thread, other threads:[~2020-09-27 8:10 UTC | newest]
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