* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis-bin/
@ 2014-03-23 19:10 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2014-03-23 19:10 UTC (permalink / raw
To: gentoo-commits
commit: 116a34b4a030050965fddb6fda334062ef424105
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 19:09:18 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 19:09:18 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=116a34b4
sci-biology/artemis-bin: version bump, added a link to INSTALL docs
Package-Manager: portage-2.2.7
---
sci-biology/artemis-bin/ChangeLog | 9 +++++++--
...emis-bin-13.2.12.ebuild => artemis-bin-16.0.6.ebuild} | 16 +++++++++++++---
2 files changed, 20 insertions(+), 5 deletions(-)
diff --git a/sci-biology/artemis-bin/ChangeLog b/sci-biology/artemis-bin/ChangeLog
index 9885717..6cd5bd4 100644
--- a/sci-biology/artemis-bin/ChangeLog
+++ b/sci-biology/artemis-bin/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-biology/artemis-bin
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*artemis-bin-16.0.6 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +artemis-bin-16.0.6.ebuild, -artemis-bin-13.2.12.ebuild:
+ sci-biology/artemis-bin: version bump, added a link to INSTALL docs
+
03 Mar 2013; Justin Lecher <jlec@gentoo.org> artemis-bin-13.2.12.ebuild,
metadata.xml:
Clean whitespace errors
@@ -11,4 +17,3 @@
08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+artemis-bin-13.2.12.ebuild, +metadata.xml:
initial, not yet working ebuild
-
diff --git a/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild b/sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild
similarity index 51%
rename from sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild
rename to sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild
index fa1edc3..528d3e8 100644
--- a/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild
+++ b/sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild
@@ -6,9 +6,12 @@ EAPI=3
inherit java-pkg-2
+MY_V="16"
+
DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v13/v"${PV}"/artemis_compiled_v"${PV}".tar.gz"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_compiled_v"${PV}".tar.gz
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf"
LICENSE="GPL-2"
SLOT="0"
@@ -16,6 +19,13 @@ KEYWORDS=""
IUSE=""
DEPEND="sci-biology/samtools
- sci-biology/bamview"
+ sci-biology/bambino" # aka BamView
RDEPEND="${DEPEND}
- >=virtual/jre-1.5"
+ >=virtual/jre-1.6"
+
+src_install(){
+ dodoc artemis.pdf
+}
+
+# do not know what is the diffeerence between artemis_compiled_v16.0.6.tar.gz, artemis_v16.0.6.jar and sartemis_v16.0.6.jar
+# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.6/
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis-bin/
@ 2017-01-29 14:20 Justin Lecher
0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2017-01-29 14:20 UTC (permalink / raw
To: gentoo-commits
commit: 8a654b4c4acd6785edbf734153ac08234d8a13de
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 29 13:57:35 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 29 13:57:35 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=8a654b4c
sci-biology/artemis-bin: 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/artemis-bin/artemis-bin-16.0.11.ebuild | 8 +++++---
sci-biology/artemis-bin/metadata.xml | 2 +-
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
index 2949569..2f1529a 100644
--- a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
+++ b/sci-biology/artemis-bin/artemis-bin-16.0.11.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
# $Id$
@@ -10,12 +10,14 @@ MY_V="16"
DESCRIPTION="DNA sequence viewer, annotation (Artemis) without comparison (ACT) tool"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_compiled_v"${PV}".tar.gz
+SRC_URI="
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_compiled_v"${PV}".tar.gz
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_v"${PV}".jar
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/sartemis_v"${PV}".jar
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/artemis_manual_complete.pdf -> ${P}.manual.pdf
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/release_notes.txt -> ${P}.release_notes.txt
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/art_html_build.zip -> ${P}.html_build.zip"
+
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
@@ -25,7 +27,7 @@ S="${WORKDIR}"
DEPEND="
!sci-biology/artemis
- sci-biology/samtools"
+ sci-biology/samtools:0"
RDEPEND="${DEPEND}
>=virtual/jre-1.6"
diff --git a/sci-biology/artemis-bin/metadata.xml b/sci-biology/artemis-bin/metadata.xml
index 1699e58..f68a1b6 100644
--- a/sci-biology/artemis-bin/metadata.xml
+++ b/sci-biology/artemis-bin/metadata.xml
@@ -5,7 +5,7 @@
<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>
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis-bin/
@ 2016-03-30 14:26 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2016-03-30 14:26 UTC (permalink / raw
To: gentoo-commits
commit: 0686691e7ff66f89c32e2933701712f20d920dc9
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 30 14:22:54 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 30 14:22:54 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0686691e
sci-biology/artemis-bin: install docs, cleanup ebuild and bring it in sync with sci-biology/act-bin and sci-biology/artemis-9999
Package-Manager: portage-2.2.28
sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
index 7f5a97b..2949569 100644
--- a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
+++ b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis-bin/
@ 2016-03-30 14:26 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2016-03-30 14:26 UTC (permalink / raw
To: gentoo-commits
commit: f020b550bf8bf4e51784679da95213ed2a50bc23
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 30 14:22:08 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 30 14:22:08 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f020b550
sci-biology/artemis-bin: install docs, cleanup ebuild and bring it in sync with sci-biology/act-bin and sci-biology/artemis-9999
Package-Manager: portage-2.2.28
sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild | 27 ++++++++++++++++++----
1 file changed, 22 insertions(+), 5 deletions(-)
diff --git a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
index e0c9fe9..7f5a97b 100644
--- a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
+++ b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
@@ -2,24 +2,26 @@
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit java-pkg-2
MY_V="16"
-DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool"
+DESCRIPTION="DNA sequence viewer, annotation (Artemis) without comparison (ACT) tool"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_compiled_v"${PV}".tar.gz
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_v"${PV}".jar
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/sartemis_v"${PV}".jar
- ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf"
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/artemis_manual_complete.pdf -> ${P}.manual.pdf
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/release_notes.txt -> ${P}.release_notes.txt
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/art_html_build.zip -> ${P}.html_build.zip"
LICENSE="GPL-2"
SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-S="${WORKDIR}"/artemis
+S="${WORKDIR}"
DEPEND="
!sci-biology/artemis
@@ -27,12 +29,24 @@ DEPEND="
RDEPEND="${DEPEND}
>=virtual/jre-1.6"
+src_unpack(){
+ unzip "${DISTDIR}"/${P}.html_build.zip || die
+}
+
+src_prepare(){
+ default
+ cd art_html_build || die
+ rm -f .DS_Store HTML.index HTML.manifest || die
+}
+
src_install(){
cp -p "${DISTDIR}"/artemis_v"${PV}".jar artemis.jar || die
java-pkg_dojar artemis.jar
cp -p "${DISTDIR}"/sartemis_v"${PV}".jar sartemis.jar || die
java-pkg_dojar sartemis.jar
- dodoc "${DISTDIR}"/artemis.pdf README
+ dodoc "${DISTDIR}"/${P}.manual.pdf "${DISTDIR}"/${P}.release_notes.txt
+ insinto /usr/share/doc/"${PN}"/html
+ doins art_html_build/*
}
# artemis_compiled_v16.0.11.tar.gz contains compiled binaries but also java *.class files
@@ -41,4 +55,7 @@ src_install(){
pkg_postinst(){
einfo "For BAM file support please install sci-biology/BamView"
+ einfo "You may find interesting the additional web resources:"
+ einfo "http://www.webact.org/WebACT"
+ einfo "http://www.hpa-bioinfotools.org.uk/pise/double_act.html"
}
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis-bin/
@ 2015-06-09 10:25 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-06-09 10:25 UTC (permalink / raw
To: gentoo-commits
commit: 9e3dc1d39ddeb3791dd2f71f9eb6087bf0ba61c4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jun 9 10:22:32 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jun 9 10:22:32 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9e3dc1d3
sci-biology/artemis-bin: ebuild cleanup
Package-Manager: portage-2.2.18
sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild | 29 ++++++++++++++++------
1 file changed, 21 insertions(+), 8 deletions(-)
diff --git a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
index d089c7f..3c04159 100644
--- a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
+++ b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
@@ -10,22 +10,35 @@ MY_V="16"
DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
-SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_compiled_v"${PV}".tar.gz
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_compiled_v"${PV}".tar.gz
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/artemis_v"${PV}".jar
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v"${MY_V}"/v"${PV}"/sartemis_v"${PV}".jar
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf"
-
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS=""
+KEYWORDS="~amd64"
IUSE=""
-DEPEND="sci-biology/samtools
- sci-biology/BamView"
+S="${WORKDIR}"/artemis
+
+DEPEND="
+ !sci-biology/artemis
+ sci-biology/samtools"
RDEPEND="${DEPEND}
>=virtual/jre-1.6"
src_install(){
- dodoc artemis.pdf
+ cp -p "${DISTDIR}"/artemis_v"${PV}".jar artemis.jar || die
+ java-pkg_dojar artemis.jar
+ cp -p "${DISTDIR}"/sartemis_v"${PV}".jar sartemis.jar || die
+ java-pkg_dojar sartemis.jar
+ dodoc "${DISTDIR}"/artemis.pdf README
}
-# do not know what is the diffeerence between artemis_compiled_v16.0.6.tar.gz, artemis_v16.0.6.jar and sartemis_v16.0.6.jar
-# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.6/
+# artemis_compiled_v16.0.11.tar.gz contains compiled binaries but also java *.class files
+# artemis_v16.0.11.jar and sartemis_v16.0.11.jar
+# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/v16.0.11/
+
+pkg_postinst(){
+ einfo "For BAM file support please install sci-biology/BamView"
+}
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis-bin/
@ 2015-05-02 16:29 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-05-02 16:29 UTC (permalink / raw
To: gentoo-commits
commit: daa8e65741c2232b3f5abe9fc7fceefc0f734b6e
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat May 2 16:20:42 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat May 2 16:20:42 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=daa8e657
sci-biology/artemis-bin: EAPI bump
Package-Manager: portage-2.2.18
sci-biology/artemis-bin/ChangeLog | 4 ++++
sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/artemis-bin/ChangeLog b/sci-biology/artemis-bin/ChangeLog
index d1286af..4320cdc 100644
--- a/sci-biology/artemis-bin/ChangeLog
+++ b/sci-biology/artemis-bin/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 02 May 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ artemis-bin-16.0.11.ebuild:
+ sci-biology/artemis-bin: EAPI bump
+
*artemis-bin-16.0.11 (08 Jan 2015)
08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
index 69b26ca..d089c7f 100644
--- a/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
+++ b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
@@ -2,7 +2,7 @@
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
inherit java-pkg-2
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis-bin/
@ 2015-01-08 20:03 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2015-01-08 20:03 UTC (permalink / raw
To: gentoo-commits
commit: 902de4731da00d5ebc86830c3589fd9575aebd66
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 8 20:01:45 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 8 20:01:45 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=902de473
sci-biology/artemis-bin: version bump
Package-Manager: portage-2.2.7
---
sci-biology/artemis-bin/ChangeLog | 8 +++++++-
.../{artemis-bin-16.0.6.ebuild => artemis-bin-16.0.11.ebuild} | 2 +-
2 files changed, 8 insertions(+), 2 deletions(-)
diff --git a/sci-biology/artemis-bin/ChangeLog b/sci-biology/artemis-bin/ChangeLog
index c5c5379..d1286af 100644
--- a/sci-biology/artemis-bin/ChangeLog
+++ b/sci-biology/artemis-bin/ChangeLog
@@ -1,7 +1,13 @@
# ChangeLog for sci-biology/artemis-bin
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*artemis-bin-16.0.11 (08 Jan 2015)
+
+ 08 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +artemis-bin-16.0.11.ebuild, -artemis-bin-16.0.6.ebuild:
+ sci-biology/artemis-bin: version bump
+
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
artemis-bin-16.0.6.ebuild:
sci-biology/artemis-bin: documented dependences
diff --git a/sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild b/sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
similarity index 95%
rename from sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild
rename to sci-biology/artemis-bin/artemis-bin-16.0.11.ebuild
index 2d738cb..69b26ca 100644
--- a/sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild
+++ b/sci-biology/artemis-bin/artemis-bin-16.0.11.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] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis-bin/
@ 2014-03-23 23:03 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2014-03-23 23:03 UTC (permalink / raw
To: gentoo-commits
commit: 0958e532db4f1ad484f490bb16a4c6d2997c9172
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 23:02:08 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 23:02:08 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=0958e532
sci-biology/artemis-bin: documented dependences
Package-Manager: portage-2.2.7
---
sci-biology/artemis-bin/ChangeLog | 4 ++++
sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild | 2 +-
2 files changed, 5 insertions(+), 1 deletion(-)
diff --git a/sci-biology/artemis-bin/ChangeLog b/sci-biology/artemis-bin/ChangeLog
index 6cd5bd4..c5c5379 100644
--- a/sci-biology/artemis-bin/ChangeLog
+++ b/sci-biology/artemis-bin/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ artemis-bin-16.0.6.ebuild:
+ sci-biology/artemis-bin: documented dependences
+
*artemis-bin-16.0.6 (23 Mar 2014)
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild b/sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild
index 528d3e8..2d738cb 100644
--- a/sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild
+++ b/sci-biology/artemis-bin/artemis-bin-16.0.6.ebuild
@@ -19,7 +19,7 @@ KEYWORDS=""
IUSE=""
DEPEND="sci-biology/samtools
- sci-biology/bambino" # aka BamView
+ sci-biology/BamView"
RDEPEND="${DEPEND}
>=virtual/jre-1.6"
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis-bin/
@ 2013-03-03 17:52 Justin Lecher
0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2013-03-03 17:52 UTC (permalink / raw
To: gentoo-commits
commit: c7a9811a6a28fbf9b91ce1d6188a27951db8813a
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Mar 3 16:32:53 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Mar 3 16:32:53 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=c7a9811a
sci-biology/artemis-bin: Clean whitespace errors
Package-Manager: portage-2.2.0_alpha164
---
sci-biology/artemis-bin/ChangeLog | 6 +++++-
sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild | 3 +--
sci-biology/artemis-bin/metadata.xml | 10 +++++-----
3 files changed, 11 insertions(+), 8 deletions(-)
diff --git a/sci-biology/artemis-bin/ChangeLog b/sci-biology/artemis-bin/ChangeLog
index 9659b90..9885717 100644
--- a/sci-biology/artemis-bin/ChangeLog
+++ b/sci-biology/artemis-bin/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/artemis-bin
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 03 Mar 2013; Justin Lecher <jlec@gentoo.org> artemis-bin-13.2.12.ebuild,
+ metadata.xml:
+ Clean whitespace errors
+
*artemis-bin-13.2.12 (08 Jan 2012)
08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild b/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild
index a62f700..e457ac8 100644
--- a/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild
+++ b/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2013 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
@@ -19,4 +19,3 @@ DEPEND="sci-biology/samtools
sci-biology/bamview"
RDEPEND="${DEPEND}
>=virtual/jre-1.5"
-
diff --git a/sci-biology/artemis-bin/metadata.xml b/sci-biology/artemis-bin/metadata.xml
index 07b5255..2bc8930 100644
--- a/sci-biology/artemis-bin/metadata.xml
+++ b/sci-biology/artemis-bin/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>
^ permalink raw reply related [flat|nested] 10+ messages in thread* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis-bin/
@ 2012-01-08 15:51 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2012-01-08 15:51 UTC (permalink / raw
To: gentoo-commits
commit: f08d29fa794de7b2c607e92d197a7d5b3605a5bc
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan 8 15:51:07 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jan 8 15:51:07 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=f08d29fa
sci-biology/artemis-bin: DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool
---
sci-biology/artemis-bin/ChangeLog | 10 +++++++++
sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild | 22 ++++++++++++++++++++
sci-biology/artemis-bin/metadata.xml | 9 ++++++++
3 files changed, 41 insertions(+), 0 deletions(-)
diff --git a/sci-biology/artemis-bin/ChangeLog b/sci-biology/artemis-bin/ChangeLog
new file mode 100644
index 0000000..9659b90
--- /dev/null
+++ b/sci-biology/artemis-bin/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/artemis-bin
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*artemis-bin-13.2.12 (08 Jan 2012)
+
+ 08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +artemis-bin-13.2.12.ebuild, +metadata.xml:
+ initial, not yet working ebuild
+
diff --git a/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild b/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild
new file mode 100644
index 0000000..a62f700
--- /dev/null
+++ b/sci-biology/artemis-bin/artemis-bin-13.2.12.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit java-pkg-2
+
+DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v13/v"${PV}"/artemis_compiled_v"${PV}".tar.gz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS=""
+IUSE=""
+
+DEPEND="sci-biology/samtools
+ sci-biology/bamview"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.5"
+
diff --git a/sci-biology/artemis-bin/metadata.xml b/sci-biology/artemis-bin/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/artemis-bin/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] 10+ messages in thread
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