* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas2/
@ 2014-03-23 21:14 Martin Mokrejs
0 siblings, 0 replies; 8+ messages in thread
From: Martin Mokrejs @ 2014-03-23 21:14 UTC (permalink / raw
To: gentoo-commits
commit: 9eb2c98e084ad39a175118774bad2e0fd587057d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 21:13:39 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 21:13:39 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9eb2c98e
sci-biology/Atlas2: a skeleton for a new package, needs help from ruby team
---
sci-biology/Atlas2/Atlas2-1.4.3.ebuild | 41 ++++++++++++++++++++++++++++++++++
sci-biology/Atlas2/ChangeLog | 10 +++++++++
sci-biology/Atlas2/metadata.xml | 9 ++++++++
3 files changed, 60 insertions(+)
diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
new file mode 100644
index 0000000..7e2049d
--- /dev/null
+++ b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+USE_RUBY="ruby19 ruby20"
+
+inherit ruby-fakegem
+
+DESCRIPTION="Variant analysis tools (true SNPs, insertions, deletions) from whole exome capture sequencing (WECS)"
+HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas2"
+SRC_URI="http://downloads.sourceforge.net/project/atlas2/Atlas2_v1.4.3.zip"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="dev-lang/ruby
+ sci-biology/samtools
+ sci-biology/blat
+ sci-biology/phrap
+ sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/all/"${PN}"_v"${PV}"
+
+src_compile(){
+ cd SOLiD-SNP-caller || die
+ emake
+
+ cd ../vcfPrinter
+ # TODO: install the *.rb files
+
+ cd ../Atlas-Indel2
+ # TODO: install the *.rb and files in lib/
+
+ cd ../Atlas-SNP2
+ # TODO: install
+}
diff --git a/sci-biology/Atlas2/ChangeLog b/sci-biology/Atlas2/ChangeLog
new file mode 100644
index 0000000..65bee22
--- /dev/null
+++ b/sci-biology/Atlas2/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/Atlas2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*Atlas2-1.4.3 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +Atlas2-1.4.3.ebuild, +metadata.xml:
+ a skeleton for a new package, needs help from ruby team
+
diff --git a/sci-biology/Atlas2/metadata.xml b/sci-biology/Atlas2/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/Atlas2/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] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas2/
@ 2015-09-23 12:48 Justin Lecher
0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2015-09-23 12:48 UTC (permalink / raw
To: gentoo-commits
commit: a8668a8fb4aeab16f129654acc1b8465c04f17a0
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Sep 23 12:46:06 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Sep 23 12:46:06 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a8668a8f
sci-biology/Atlas2: Use default functions
Package-Manager: portage-2.2.21
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/Atlas2/Atlas2-1.4.3.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
index fe35835..4e27e89 100644
--- a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
+++ b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
@@ -28,7 +28,7 @@ S="${WORKDIR}"/all/"${PN}"_v"${PV}"
src_compile(){
cd SOLiD-SNP-caller || die
- emake
+ default
cd ../vcfPrinter
# TODO: install the *.rb files
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas2/
@ 2015-12-25 21:18 Marius Brehler
0 siblings, 0 replies; 8+ messages in thread
From: Marius Brehler @ 2015-12-25 21:18 UTC (permalink / raw
To: gentoo-commits
commit: 8223dfff412cfb14e0589ddf6183ed84d9c20a76
Author: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Fri Dec 25 21:18:09 2015 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Fri Dec 25 21:18:09 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8223dfff
sci-biology/Atlas2: Drop ruby19, shorten description, add missing dies
Package-Manager: portage-2.2.24
sci-biology/Atlas2/Atlas2-1.4.3.ebuild | 10 +++++-----
sci-biology/Atlas2/ChangeLog | 3 +++
2 files changed, 8 insertions(+), 5 deletions(-)
diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
index 4e27e89..6b82ca4 100644
--- a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
+++ b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
@@ -4,11 +4,11 @@
EAPI=5
-USE_RUBY="ruby19 ruby20"
+USE_RUBY="ruby20"
inherit ruby-fakegem
-DESCRIPTION="Variant analysis tools (true SNPs, insertions, deletions) from whole exome capture sequencing (WECS)"
+DESCRIPTION="Variant analysis tools from whole exome capture sequencing (WECS)"
HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas2"
SRC_URI="http://downloads.sourceforge.net/project/atlas2/Atlas2_v1.4.3.zip"
@@ -30,12 +30,12 @@ src_compile(){
cd SOLiD-SNP-caller || die
default
- cd ../vcfPrinter
+ cd ../vcfPrinter || die
# TODO: install the *.rb files
- cd ../Atlas-Indel2
+ cd ../Atlas-Indel2 || die
# TODO: install the *.rb and files in lib/
- cd ../Atlas-SNP2
+ cd ../Atlas-SNP2 || die
# TODO: install
}
diff --git a/sci-biology/Atlas2/ChangeLog b/sci-biology/Atlas2/ChangeLog
index f6b72a7..834464d 100644
--- a/sci-biology/Atlas2/ChangeLog
+++ b/sci-biology/Atlas2/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> Atlas2-1.4.3.ebuild:
+ sci-biology/Atlas2: Drop ruby19, shorten description, add missing dies
+
25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> metadata.xml:
sci-biology/Atlas2: Add longdescription
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas2/
@ 2015-12-25 21:18 Marius Brehler
0 siblings, 0 replies; 8+ messages in thread
From: Marius Brehler @ 2015-12-25 21:18 UTC (permalink / raw
To: gentoo-commits
commit: 49d09fb1dc53dafc4fa7c8dcd65e3a5a0b9ee2f8
Author: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
AuthorDate: Fri Dec 25 21:17:28 2015 +0000
Commit: Marius Brehler <marbre <AT> linux <DOT> sungazer <DOT> de>
CommitDate: Fri Dec 25 21:17:28 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=49d09fb1
sci-biology/Atlas2: Add longdescription
Package-Manager: portage-2.2.24
sci-biology/Atlas2/ChangeLog | 3 +++
sci-biology/Atlas2/metadata.xml | 6 ++++++
2 files changed, 9 insertions(+)
diff --git a/sci-biology/Atlas2/ChangeLog b/sci-biology/Atlas2/ChangeLog
index 1983165..f6b72a7 100644
--- a/sci-biology/Atlas2/ChangeLog
+++ b/sci-biology/Atlas2/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Id$
+ 25 Dec 2015; Marius Brehler <marbre@linux.sungazer.de> metadata.xml:
+ sci-biology/Atlas2: Add longdescription
+
18 Feb 2015; Justin Lecher <jlec@gentoo.org> Atlas2-1.4.3.ebuild:
sci-biology/Atlas2: Fix ruby deps
diff --git a/sci-biology/Atlas2/metadata.xml b/sci-biology/Atlas2/metadata.xml
index b6165f3..ff9e8ae 100644
--- a/sci-biology/Atlas2/metadata.xml
+++ b/sci-biology/Atlas2/metadata.xml
@@ -6,6 +6,12 @@
<email>mmokrejs@fold.natur.cuni.cz</email>
<name>Martin Mokrejs</name>
</maintainer>
+ <longdescription>
+ Atlas2 is a next-generation sequencing suite of variant analysis
+ tools specializing in the separation of true SNPs and insertions
+ and deletions (indels) from sequencing and mapping errors in Whole
+ Exome Capture Sequencing (WECS) data.
+ </longdescription>
<upstream>
<remote-id type="sourceforge">downloads</remote-id>
</upstream>
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas2/
@ 2017-01-29 14:20 Justin Lecher
0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2017-01-29 14:20 UTC (permalink / raw
To: gentoo-commits
commit: b734f44afd680893dc0e197d71fb5aca60f85629
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 29 12:31:55 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 29 12:31:55 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=b734f44a
sci-biology/Atlas2: Add missing slot operator
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/Atlas2/Atlas2-1.4.3.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
index 6b82ca4..94f226f 100644
--- a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
+++ b/sci-biology/Atlas2/Atlas2-1.4.3.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
# $Id$
@@ -18,7 +18,7 @@ KEYWORDS=""
IUSE=""
DEPEND="
- sci-biology/samtools
+ sci-biology/samtools:0
sci-biology/blat
sci-biology/phrap
sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas2/
@ 2017-02-26 8:48 Justin Lecher
0 siblings, 0 replies; 8+ messages in thread
From: Justin Lecher @ 2017-02-26 8:48 UTC (permalink / raw
To: gentoo-commits
commit: a00b613c1985e74a9b9ada3ff877bc3df2d7a828
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 26 08:43:57 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 26 08:48:51 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a00b613c
sci-biology/Atlas2: Bump Ruby version and EAPI
Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
sci-biology/Atlas2/Atlas2-1.4.3.ebuild | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
index e9b81858d..bb03640e8 100644
--- a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
+++ b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
@@ -1,9 +1,9 @@
# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
-USE_RUBY="ruby20"
+USE_RUBY="ruby21"
inherit ruby-fakegem
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas2/
@ 2017-09-02 11:55 David Seifert
0 siblings, 0 replies; 8+ messages in thread
From: David Seifert @ 2017-09-02 11:55 UTC (permalink / raw
To: gentoo-commits
commit: 44f0c9ab74846895c865a3dcde1a459b926585d7
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Sat Sep 2 11:55:15 2017 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Sat Sep 2 11:55:15 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=44f0c9ab
sci-biology/Atlas2: Update USE_RUBY to fix breakages
Package-Manager: Portage-2.3.8, Repoman-2.3.3
sci-biology/Atlas2/Atlas2-1.4.3.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
index bb03640e8..2305fb15d 100644
--- a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
+++ b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
@@ -3,7 +3,7 @@
EAPI=6
-USE_RUBY="ruby21"
+USE_RUBY="ruby22 ruby23 ruby24"
inherit ruby-fakegem
^ permalink raw reply related [flat|nested] 8+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/Atlas2/
@ 2020-09-27 22:43 Horea Christian
0 siblings, 0 replies; 8+ messages in thread
From: Horea Christian @ 2020-09-27 22:43 UTC (permalink / raw
To: gentoo-commits
commit: 1a7addf40ba3a1e97f3fefe12d9b71086f954c71
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 22:35:48 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 22:43:20 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=1a7addf4
sci-biology/Atlas2: removed discontinued package
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/Atlas2/Atlas2-1.4.3.ebuild | 40 ----------------------------------
sci-biology/Atlas2/metadata.xml | 21 ------------------
2 files changed, 61 deletions(-)
diff --git a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild b/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
deleted file mode 100644
index 2305fb15d..000000000
--- a/sci-biology/Atlas2/Atlas2-1.4.3.ebuild
+++ /dev/null
@@ -1,40 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-USE_RUBY="ruby22 ruby23 ruby24"
-
-inherit ruby-fakegem
-
-DESCRIPTION="Variant analysis tools from whole exome capture sequencing (WECS)"
-HOMEPAGE="https://www.hgsc.bcm.edu/software/atlas2"
-SRC_URI="http://downloads.sourceforge.net/project/atlas2/Atlas2_v1.4.3.zip"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND="
- sci-biology/samtools:0
- sci-biology/blat
- sci-biology/phrap
- sci-biology/ucsc-genome-browser" # that provides bigWig.h and jkweb.a, aka Jim Kent's src
-RDEPEND="${DEPEND}"
-
-S="${WORKDIR}"/all/"${PN}"_v"${PV}"
-
-src_compile(){
- cd SOLiD-SNP-caller || die
- default
-
- cd ../vcfPrinter || die
- # TODO: install the *.rb files
-
- cd ../Atlas-Indel2 || die
- # TODO: install the *.rb and files in lib/
-
- cd ../Atlas-SNP2 || die
- # TODO: install
-}
diff --git a/sci-biology/Atlas2/metadata.xml b/sci-biology/Atlas2/metadata.xml
deleted file mode 100644
index 7ce5225f5..000000000
--- a/sci-biology/Atlas2/metadata.xml
+++ /dev/null
@@ -1,21 +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>
- <longdescription>
-Atlas2 is a next-generation sequencing suite of variant analysis
-tools specializing in the separation of true SNPs and insertions
-and deletions (indels) from sequencing and mapping errors in Whole
-Exome Capture Sequencing (WECS) data.
-</longdescription>
- <upstream>
- <remote-id type="sourceforge">downloads</remote-id>
- </upstream>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 8+ messages in thread
end of thread, other threads:[~2020-09-27 22:43 UTC | newest]
Thread overview: 8+ messages (download: mbox.gz follow: Atom feed
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2014-03-23 21:14 Martin Mokrejs
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