* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis/
@ 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: 1afb461b204933db48bfe976a37203c92846930d
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Jan 8 15:49:57 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Jan 8 15:49:57 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1afb461b
sci-biology/artemis: DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool
---
sci-biology/artemis/ChangeLog | 10 ++++++++
sci-biology/artemis/artemis-9999.ebuild | 39 +++++++++++++++++++++++++++++++
sci-biology/artemis/metadata.xml | 9 +++++++
3 files changed, 58 insertions(+), 0 deletions(-)
diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog
new file mode 100644
index 0000000..8a33496
--- /dev/null
+++ b/sci-biology/artemis/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/artemis
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*artemis-9999 (08 Jan 2012)
+
+ 08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +artemis-9999.ebuild, +metadata.xml:
+ initial, not yet working ebuild
+
diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
new file mode 100644
index 0000000..ff8d52d
--- /dev/null
+++ b/sci-biology/artemis/artemis-9999.ebuild
@@ -0,0 +1,39 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=3
+
+inherit java-pkg-2 java-ant-2
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool"
+HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
+
+if [ "$PV" == "9999" ]; then
+ EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
+ KEYWORDS=""
+else
+ SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v13/v"${PV}"/artemis_compiled_v"${PV}".tar.gz"
+ KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND="sci-biology/samtools
+ sci-biology/bamview
+ >=virtual/jdk-1.5
+ >=dev-java/sun-jdk-1.5
+ dev-java/ant-core"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.5"
+
+src_compile() {
+ ant compile || die
+
+ einfo "Need to figure out where does the GeneBuilder application come from so that one could use Chado for automated gene prediction pipeline"
+}
diff --git a/sci-biology/artemis/metadata.xml b/sci-biology/artemis/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/artemis/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
* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis/
@ 2012-02-07 23:45 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2012-02-07 23:45 UTC (permalink / raw
To: gentoo-commits
commit: aa6b1c5670c52a5cfe62645536c4eace8eec862d
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 7 23:45:14 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 7 23:45:14 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=aa6b1c56
sci-biology/artemis: adjust ebuild based on upstream providing a Makefile
(Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
---
sci-biology/artemis/ChangeLog | 3 +++
sci-biology/artemis/artemis-9999.ebuild | 4 ++--
2 files changed, 5 insertions(+), 2 deletions(-)
diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog
index a87b1e4..a992d60 100644
--- a/sci-biology/artemis/ChangeLog
+++ b/sci-biology/artemis/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild:
+ sci-biology/artemis: adjust ebuild based on upstream providing a Makefile
+
07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
artemis-9999.ebuild:
adjust ebuild based on upstream providing a Makefile
diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
index 4739ad8..4481975 100644
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ b/sci-biology/artemis/artemis-9999.ebuild
@@ -13,7 +13,7 @@ HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
if [ "$PV" == "9999" ]; then
EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
- KEYWORDS=""
+ KEYWORDS="~amd64 ~x86"
else
SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v13/v"${PV}"/artemis_compiled_v"${PV}".tar.gz"
KEYWORDS="~amd64 ~x86"
@@ -21,7 +21,7 @@ fi
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS=""
IUSE=""
# uses its own BamView
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis/
@ 2012-02-07 23:45 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2012-02-07 23:45 UTC (permalink / raw
To: gentoo-commits
commit: 11ae7cf4d443b53e4a1f90391c0a743ed5698a6a
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Feb 7 23:44:33 2012 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Feb 7 23:44:33 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=11ae7cf4
sci-biology/artemis: adjust ebuild based on upstream providing a Makefile
(Portage version: 2.1.10.45/git/Linux x86_64, unsigned Manifest commit)
---
sci-biology/artemis/ChangeLog | 4 ++++
sci-biology/artemis/artemis-9999.ebuild | 8 ++++++--
2 files changed, 10 insertions(+), 2 deletions(-)
diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog
index 8a33496..a87b1e4 100644
--- a/sci-biology/artemis/ChangeLog
+++ b/sci-biology/artemis/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ artemis-9999.ebuild:
+ adjust ebuild based on upstream providing a Makefile
+
*artemis-9999 (08 Jan 2012)
08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
index ff8d52d..4739ad8 100644
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ b/sci-biology/artemis/artemis-9999.ebuild
@@ -24,16 +24,20 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE=""
+# uses its own BamView
DEPEND="sci-biology/samtools
- sci-biology/bamview
>=virtual/jdk-1.5
>=dev-java/sun-jdk-1.5
dev-java/ant-core"
RDEPEND="${DEPEND}
>=virtual/jre-1.5"
+# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00551.html
+# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00561.html
+# http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial
src_compile() {
- ant compile || die
+ emake || die
+ # ant compile || die
einfo "Need to figure out where does the GeneBuilder application come from so that one could use Chado for automated gene prediction pipeline"
}
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis/
@ 2014-01-06 19:27 Justin Lecher
0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2014-01-06 19:27 UTC (permalink / raw
To: gentoo-commits
commit: 420e46ff1a1f7709757fae778140fb53c24189d0
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Jan 6 19:02:45 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Jan 6 19:02:45 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=420e46ff
sci-biology/artemis: Switch from git-2 to git-r3
Package-Manager: portage-2.2.8
---
sci-biology/artemis/ChangeLog | 6 +++++-
sci-biology/artemis/artemis-9999.ebuild | 34 ++++++++++-----------------------
sci-biology/artemis/metadata.xml | 10 +++++-----
3 files changed, 20 insertions(+), 30 deletions(-)
diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog
index a992d60..56cbedc 100644
--- a/sci-biology/artemis/ChangeLog
+++ b/sci-biology/artemis/ChangeLog
@@ -1,7 +1,11 @@
# ChangeLog for sci-biology/artemis
-# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 06 Jan 2014; Justin Lecher <jlec@gentoo.org> artemis-9999.ebuild,
+ metadata.xml:
+ Switch from git-2 to git-r3
+
07 Feb 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild:
sci-biology/artemis: adjust ebuild based on upstream providing a Makefile
diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
index 4481975..ca3ddf1 100644
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ b/sci-biology/artemis/artemis-9999.ebuild
@@ -1,23 +1,15 @@
-# Copyright 1999-2012 Gentoo Foundation
+# Copyright 1999-2014 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Header: $
-EAPI=3
+EAPI=5
-inherit java-pkg-2 java-ant-2
-
-[ "$PV" == "9999" ] && inherit git-2
+inherit java-pkg-2 java-ant-2 git-r3
DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
-
-if [ "$PV" == "9999" ]; then
- EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
- KEYWORDS="~amd64 ~x86"
-else
- SRC_URI="ftp://ftp.sanger.ac.uk/pub4/resources/software/artemis/v13/v"${PV}"/artemis_compiled_v"${PV}".tar.gz"
- KEYWORDS="~amd64 ~x86"
-fi
+SRC_URI=""
+EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
LICENSE="GPL-2"
SLOT="0"
@@ -25,19 +17,13 @@ KEYWORDS=""
IUSE=""
# uses its own BamView
-DEPEND="sci-biology/samtools
- >=virtual/jdk-1.5
- >=dev-java/sun-jdk-1.5
- dev-java/ant-core"
+DEPEND="
+ sci-biology/samtools
+ >=virtual/jdk-1.5
+ dev-java/ant-core"
RDEPEND="${DEPEND}
- >=virtual/jre-1.5"
+ >=virtual/jre-1.5"
# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00551.html
# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00561.html
# http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial
-src_compile() {
- emake || die
- # ant compile || die
-
- einfo "Need to figure out where does the GeneBuilder application come from so that one could use Chado for automated gene prediction pipeline"
-}
diff --git a/sci-biology/artemis/metadata.xml b/sci-biology/artemis/metadata.xml
index 07b5255..2bc8930 100644
--- a/sci-biology/artemis/metadata.xml
+++ b/sci-biology/artemis/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/
@ 2014-03-23 19:19 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2014-03-23 19:19 UTC (permalink / raw
To: gentoo-commits
commit: 9e9bd7a06a42132862b494a317715200c0503f19
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 19:11:10 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 19:11:10 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=9e9bd7a0
sci-biology/artemis: fixed JVM dependency, added a link to INSTALL docs
Package-Manager: portage-2.2.7
---
sci-biology/artemis/ChangeLog | 4 +++-
sci-biology/artemis/artemis-9999.ebuild | 6 ++++--
2 files changed, 7 insertions(+), 3 deletions(-)
diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog
index 56cbedc..4054aa1 100644
--- a/sci-biology/artemis/ChangeLog
+++ b/sci-biology/artemis/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild:
+ sci-biology/artemis: fixed JVM dependency, added a link to INSTALL docs
+
06 Jan 2014; Justin Lecher <jlec@gentoo.org> artemis-9999.ebuild,
metadata.xml:
Switch from git-2 to git-r3
@@ -18,4 +21,3 @@
08 Jan 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+artemis-9999.ebuild, +metadata.xml:
initial, not yet working ebuild
-
diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
index ca3ddf1..c1e6146 100644
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ b/sci-biology/artemis/artemis-9999.ebuild
@@ -19,11 +19,13 @@ IUSE=""
# uses its own BamView
DEPEND="
sci-biology/samtools
- >=virtual/jdk-1.5
+ >=virtual/jdk-1.6
dev-java/ant-core"
RDEPEND="${DEPEND}
- >=virtual/jre-1.5"
+ >=virtual/jre-1.6"
# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00551.html
# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00561.html
# http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial
+
+# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis/
@ 2014-03-23 23:02 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2014-03-23 23:02 UTC (permalink / raw
To: gentoo-commits
commit: 16bd6f6fb44f64a859a9c16df70bdb1e711513b7
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 23:01:27 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 23:01:27 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=16bd6f6f
sci-biology/artemis: documented dependences
Package-Manager: portage-2.2.7
---
sci-biology/artemis/ChangeLog | 3 +++
sci-biology/artemis/artemis-9999.ebuild | 2 ++
2 files changed, 5 insertions(+)
diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog
index 4054aa1..86fc7ce 100644
--- a/sci-biology/artemis/ChangeLog
+++ b/sci-biology/artemis/ChangeLog
@@ -3,6 +3,9 @@
# $Header: $
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild:
+ sci-biology/artemis: documented dependences
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild:
sci-biology/artemis: fixed JVM dependency, added a link to INSTALL docs
06 Jan 2014; Justin Lecher <jlec@gentoo.org> artemis-9999.ebuild,
diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
index c1e6146..fc90424 100644
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ b/sci-biology/artemis/artemis-9999.ebuild
@@ -29,3 +29,5 @@ RDEPEND="${DEPEND}
# http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial
# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf
+
+# BamView is at http://bamview.sourceforge.net/
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis/
@ 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: d33eacc4b6316885d2d31c3ef5774bb731242cd7
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Jun 9 10:24:16 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Jun 9 10:24:16 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=d33eacc4
sci-biology/artemis: ebuild cleanup; officially there is not install and one needs to keep the structure of the source tree and execute directly from there; therefore the ebuild does not work yet
Package-Manager: portage-2.2.18
sci-biology/artemis/ChangeLog | 5 +++++
sci-biology/artemis/artemis-9999.ebuild | 38 ++++++++++++++++++++++++++++-----
2 files changed, 38 insertions(+), 5 deletions(-)
diff --git a/sci-biology/artemis/ChangeLog b/sci-biology/artemis/ChangeLog
index 4bebaff..818f34c 100644
--- a/sci-biology/artemis/ChangeLog
+++ b/sci-biology/artemis/ChangeLog
@@ -2,6 +2,11 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 09 Jun 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> artemis-9999.ebuild:
+ sci-biology/artemis: ebuild cleanup; officially there is not install and one
+ needs to keep the structure of the source tree and execute directly from
+ there; therefore the ebuild does not work yet
+
18 Feb 2015; Justin Lecher <jlec@gentoo.org> artemis-9999.ebuild:
sci-biology/artemis: fix SLOT operators
diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
index 630e392..8db5509 100644
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ b/sci-biology/artemis/artemis-9999.ebuild
@@ -6,9 +6,9 @@ EAPI=5
inherit java-pkg-2 java-ant-2 git-r3
-DESCRIPTION="DNA sequence viewer, annotation (Artemis) and comparison (ACT) tool"
+DESCRIPTION="DNA sequence viewer/annotation (Artemis) and comparison (ACT) tool"
HOMEPAGE="http://www.sanger.ac.uk/resources/software/artemis"
-SRC_URI=""
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf"
EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
LICENSE="GPL-2"
@@ -21,13 +21,41 @@ RDEPEND="
sci-biology/samtools
>=virtual/jre-1.6:*"
DEPEND="${RDEPEND}
+ !sci-biology/artemis-bin
dev-java/ant-core
- >=virtual/jdk-1.6:*"
+ >=virtual/jdk-1.6:*
+ dev-java/log4j
+ dev-java/jdbc-postgresql
+ dev-java/jakarta-regexp
+ dev-java/batik
+ dev-java/j2ssh
+ sci-biology/picard
+ dev-java/biojava"
+# some more dependencies extracted from /usr/bin/act
+# JacORB.jar, jemAlign.jar, macos.jar, chado-14-interface.jar, iBatis, biojava.jar,
+#
# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00551.html
# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00561.html
# http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial
-# ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf
-
# BamView is at http://bamview.sourceforge.net/
+
+src_compile(){
+ ant || die
+}
+
+src_install(){
+ dobin act act.command art dnaplotter gff2embl
+ java-pkg_dojar ant-build/artemis.jar
+ dodoc "${DISTDIR}"/artemis.pdf README
+}
+
+# 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"
+ einfo " from http://bamview.sourceforge.net"
+}
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/artemis/
@ 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: 89b91efb19621ed16be8bf20cb05670120ec431d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 30 14:23:32 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 30 14:23:32 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=89b91efb
sci-biology/artemis: 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/artemis-9999.ebuild | 19 ++++++++++++++-----
1 file changed, 14 insertions(+), 5 deletions(-)
diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
index 81da9cb..d9e915d 100644
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ b/sci-biology/artemis/artemis-9999.ebuild
@@ -1,14 +1,15 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
# $Id$
-EAPI=5
+EAPI=6
inherit java-pkg-2 java-ant-2 git-r3
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/pub/resources/software/artemis/artemis.pdf"
+SRC_URI="ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf -> ${P}.manual.pdf
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/art_html_build.zip -> ${P}.html_build.zip"
EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
LICENSE="GPL-2"
@@ -41,6 +42,10 @@ DEPEND="${RDEPEND}
# BamView is at http://bamview.sourceforge.net/
+src_unpack(){
+ unzip "${DISTDIR}"/art_html_build.zip || die
+}
+
src_compile(){
ant || die
}
@@ -48,7 +53,9 @@ src_compile(){
src_install(){
dobin act act.command art dnaplotter gff2embl
java-pkg_dojar ant-build/artemis.jar
- dodoc "${DISTDIR}"/artemis.pdf README
+ dodoc "${DISTDIR}"/"${P}".manual.pdf README
+ 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
@@ -57,5 +64,7 @@ src_install(){
pkg_postinst(){
einfo "For BAM file support please install sci-biology/BamView"
- einfo " from http://bamview.sourceforge.net"
+ 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/
@ 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: 94f515f53613ad903865e2c78f394cac5e9dc65a
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Jan 29 13:56:46 2017 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Jan 29 13:56:46 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=94f515f5
sci-biology/artemis: 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/artemis-9999.ebuild | 7 ++++---
sci-biology/artemis/metadata.xml | 2 +-
2 files changed, 5 insertions(+), 4 deletions(-)
diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
index d9e915d..5d71760 100644
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ b/sci-biology/artemis/artemis-9999.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
# $Id$
@@ -8,7 +8,8 @@ inherit java-pkg-2 java-ant-2 git-r3
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/pub/resources/software/artemis/artemis.pdf -> ${P}.manual.pdf
+SRC_URI="
+ ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/artemis.pdf -> ${P}.manual.pdf
ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/art_html_build.zip -> ${P}.html_build.zip"
EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
@@ -19,7 +20,7 @@ IUSE=""
# uses its own BamView
RDEPEND="
- sci-biology/samtools
+ sci-biology/samtools:0
>=virtual/jre-1.6:*"
DEPEND="${RDEPEND}
!sci-biology/artemis-bin
diff --git a/sci-biology/artemis/metadata.xml b/sci-biology/artemis/metadata.xml
index 1699e58..f68a1b6 100644
--- a/sci-biology/artemis/metadata.xml
+++ b/sci-biology/artemis/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/
@ 2020-09-27 9:22 Horea Christian
0 siblings, 0 replies; 10+ messages in thread
From: Horea Christian @ 2020-09-27 9:22 UTC (permalink / raw
To: gentoo-commits
commit: ca7355423fa229cebfe243f837792abb9bf1ef4c
Author: Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 09:20:21 2020 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 09:20:21 2020 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=ca735542
sci-biology/artemis: remove unmaintained package
Package is not discontinued upstream, but would need a major overhaul
from present live ebuild: https://github.com/sanger-pathogens/Artemis
Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/artemis/artemis-9999.ebuild | 70 ---------------------------------
sci-biology/artemis/metadata.xml | 12 ------
2 files changed, 82 deletions(-)
diff --git a/sci-biology/artemis/artemis-9999.ebuild b/sci-biology/artemis/artemis-9999.ebuild
deleted file mode 100644
index 162cc67e7..000000000
--- a/sci-biology/artemis/artemis-9999.ebuild
+++ /dev/null
@@ -1,70 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-inherit java-pkg-2 java-ant-2 git-r3
-
-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/pub/resources/software/artemis/artemis.pdf -> ${P}.manual.pdf
- ftp://ftp.sanger.ac.uk/pub/resources/software/artemis/v16/art_html_build.zip -> ${P}.html_build.zip"
-EGIT_REPO_URI="https://github.com/sanger-pathogens/Artemis"
-
-LICENSE="GPL-2"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-# uses its own BamView
-RDEPEND="
- sci-biology/samtools:0
- >=virtual/jre-1.6:*"
-DEPEND="${RDEPEND}
- !sci-biology/artemis-bin
- dev-java/ant-core
- >=virtual/jdk-1.6:*
- dev-java/log4j
- dev-java/jdbc-postgresql
- dev-java/jakarta-regexp
- dev-java/batik
- dev-java/j2ssh
- sci-biology/picard
- dev-java/biojava"
-# some more dependencies extracted from /usr/bin/act
-# JacORB.jar, jemAlign.jar, macos.jar, chado-14-interface.jar, iBatis, biojava.jar,
-#
-
-# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00551.html
-# http://www.mail-archive.com/artemis-users@sanger.ac.uk/msg00561.html
-# http://gmod.org/wiki/Artemis-Chado_Integration_Tutorial
-
-# BamView is at http://bamview.sourceforge.net/
-
-src_unpack(){
- unzip "${DISTDIR}"/art_html_build.zip || die
-}
-
-src_compile(){
- ant || die
-}
-
-src_install(){
- dobin act act.command art dnaplotter gff2embl
- java-pkg_dojar ant-build/artemis.jar
- dodoc "${DISTDIR}"/"${P}".manual.pdf README
- insinto /usr/share/doc/"${PN}"/html
- doins art_html_build/*
-}
-
-# artemis_compiled_v16.0.11.tar.gz contains compiled binaries but also java *.class files
-# 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"
- 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"
-}
diff --git a/sci-biology/artemis/metadata.xml b/sci-biology/artemis/metadata.xml
deleted file mode 100644
index 138cb7705..000000000
--- a/sci-biology/artemis/metadata.xml
+++ /dev/null
@@ -1,12 +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>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 10+ messages in thread
end of thread, other threads:[~2020-09-27 9:22 UTC | newest]
Thread overview: 10+ messages (download: mbox.gz follow: Atom feed
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2020-09-27 9:22 Horea Christian
2016-03-30 14:26 Martin Mokrejs
2015-06-09 10:25 Martin Mokrejs
2014-03-23 23:02 Martin Mokrejs
2014-03-23 19:19 Martin Mokrejs
2014-01-06 19:27 Justin Lecher
2012-02-07 23:45 Martin Mokrejs
2012-02-07 23:45 Martin Mokrejs
2012-01-08 15:51 Martin Mokrejs
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