[gentoo-commits] proj/sci:master commit in: sci-biology/artemis-bin/

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* [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/
@ 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:     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"
 }


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* [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
 # $Id$
 


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* [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/
@ 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/
@ 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

end of thread, other threads:[~2017-01-29 14:21 UTC | newest]

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