* [gentoo-commits] proj/sci:master commit in: sci-biology/cgview-bin/
@ 2014-03-23 21:43 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2014-03-23 21:43 UTC (permalink / raw
To: gentoo-commits
commit: 078f19efedf1e0abfa70e43de79bb284aa6578dc
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 21:42:40 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 21:42:40 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=078f19ef
sci-biology/cgview-bin: new package, needs java team testing, maybe dev-java/batik is misisng svg USE flag?
Package-Manager: portage-2.2.7
---
sci-biology/cgview-bin/ChangeLog | 10 ++++++
sci-biology/cgview-bin/cgview-bin-20131130.ebuild | 44 +++++++++++++++++++++++
sci-biology/cgview-bin/metadata.xml | 9 +++++
3 files changed, 63 insertions(+)
diff --git a/sci-biology/cgview-bin/ChangeLog b/sci-biology/cgview-bin/ChangeLog
new file mode 100644
index 0000000..d8d6b14
--- /dev/null
+++ b/sci-biology/cgview-bin/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/cgview-bin
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*cgview-bin-20131130 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +cgview-bin-20131130.ebuild, +metadata.xml:
+ sci-biology/cgview-bin: new package, needs java team testing, maybe dev-
+ java/batik is misisng svg USE flag?
diff --git a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild
new file mode 100644
index 0000000..be563a9
--- /dev/null
+++ b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild
@@ -0,0 +1,44 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2
+
+# download 134MB in size!
+DESCRIPTION="CGView Comparison Tool to compare genome sequences graphically (aka CCT)"
+HOMEPAGE="http://stothard.afns.ualberta.ca/downloads/CCT"
+SRC_URI="http://www.ualberta.ca/~stothard/downloads/cgview_comparison_tool.zip"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=">=dev-lang/perl-5.8.8
+ >=sci-biology/ncbi-tools-2.2.15
+ >=virtual/jre-1.4.2
+ dev-java/xerces
+ dev-java/batik
+ dev-java/commons-lang
+ >=media-gfx/imagemagick-6
+ >=sci-biology/bioperl-1.4.0"
+RDEPEND="${DEPEND}"
+
+S="${WORKDIR}"/cgview_comparison_tool
+
+src_install() {
+ echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview_comparison_tool' > "${S}/99cgview"
+ echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview"
+ doenvd "${S}/99cgview" || die
+ #export PATH="$PATH":"${CCT_HOME}/scripts":/path/to/blast-2.2.25/bin
+ #export PERL5LIB="${CCT_HOME}"/lib/bioperl-1.2.3:"${CCT_HOME}"/lib/perl_modules:"$PERL5LIB"
+
+ dobin bin/cgview.jar
+}
+
+src_test(){
+ ./update_cogs.sh || die
+ ./test.sh || die
+}
diff --git a/sci-biology/cgview-bin/metadata.xml b/sci-biology/cgview-bin/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/cgview-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] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/cgview-bin/
@ 2015-02-18 16:41 Justin Lecher
0 siblings, 0 replies; 4+ messages in thread
From: Justin Lecher @ 2015-02-18 16:41 UTC (permalink / raw
To: gentoo-commits
commit: 7e1e46090ff9b7817cb28b62cbade16a7d58201d
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:15:20 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:15:20 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=7e1e4609
sci-biology/cgview-bin: fix SLOT operators; drop KEYWORDS as fetch failed
Package-Manager: portage-2.2.17
---
sci-biology/cgview-bin/ChangeLog | 5 +++-
sci-biology/cgview-bin/cgview-bin-20131130.ebuild | 34 +++++++++++------------
2 files changed, 21 insertions(+), 18 deletions(-)
diff --git a/sci-biology/cgview-bin/ChangeLog b/sci-biology/cgview-bin/ChangeLog
index d8d6b14..e3de215 100644
--- a/sci-biology/cgview-bin/ChangeLog
+++ b/sci-biology/cgview-bin/ChangeLog
@@ -1,7 +1,10 @@
# ChangeLog for sci-biology/cgview-bin
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Feb 2015; Justin Lecher <jlec@gentoo.org> cgview-bin-20131130.ebuild:
+ sci-biology/cgview-bin: fix SLOT operators; drop KEYWORDS as fetch failed
+
*cgview-bin-20131130 (23 Mar 2014)
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
diff --git a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild
index be563a9..61141e3 100644
--- a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild
+++ b/sci-biology/cgview-bin/cgview-bin-20131130.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: $
@@ -6,39 +6,39 @@ EAPI=5
inherit java-pkg-2
-# download 134MB in size!
DESCRIPTION="CGView Comparison Tool to compare genome sequences graphically (aka CCT)"
HOMEPAGE="http://stothard.afns.ualberta.ca/downloads/CCT"
SRC_URI="http://www.ualberta.ca/~stothard/downloads/cgview_comparison_tool.zip"
LICENSE="GPL-2"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS=""
IUSE=""
-DEPEND=">=dev-lang/perl-5.8.8
- >=sci-biology/ncbi-tools-2.2.15
- >=virtual/jre-1.4.2
- dev-java/xerces
- dev-java/batik
- dev-java/commons-lang
- >=media-gfx/imagemagick-6
- >=sci-biology/bioperl-1.4.0"
+DEPEND="
+ >=dev-lang/perl-5.8.8
+ >=sci-biology/ncbi-tools-2.2.15
+ >=virtual/jre-1.4.2:*
+ dev-java/xerces:2
+ dev-java/batik
+ dev-java/commons-lang:2.1
+ >=media-gfx/imagemagick-6
+ >=sci-biology/bioperl-1.4.0"
RDEPEND="${DEPEND}"
S="${WORKDIR}"/cgview_comparison_tool
+src_test(){
+ ./update_cogs.sh || die
+ ./test.sh || die
+}
+
src_install() {
echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview_comparison_tool' > "${S}/99cgview"
echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview"
- doenvd "${S}/99cgview" || die
+ doenvd "${S}/99cgview"
#export PATH="$PATH":"${CCT_HOME}/scripts":/path/to/blast-2.2.25/bin
#export PERL5LIB="${CCT_HOME}"/lib/bioperl-1.2.3:"${CCT_HOME}"/lib/perl_modules:"$PERL5LIB"
dobin bin/cgview.jar
}
-
-src_test(){
- ./update_cogs.sh || die
- ./test.sh || die
-}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/cgview-bin/
@ 2015-04-17 23:56 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2015-04-17 23:56 UTC (permalink / raw
To: gentoo-commits
commit: f5965a7c3727b476c3f8392bb1bec8eae7792f45
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 17 22:47:44 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 17 22:47:44 2015 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f5965a7c
sci-biology/cgview-bin: fixed installation of perl-related files
Package-Manager: portage-2.2.18
sci-biology/cgview-bin/ChangeLog | 4 ++++
sci-biology/cgview-bin/cgview-bin-20131130.ebuild | 18 +++++++++++++-----
2 files changed, 17 insertions(+), 5 deletions(-)
diff --git a/sci-biology/cgview-bin/ChangeLog b/sci-biology/cgview-bin/ChangeLog
index e3de215..3ab4181 100644
--- a/sci-biology/cgview-bin/ChangeLog
+++ b/sci-biology/cgview-bin/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 17 Apr 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ cgview-bin-20131130.ebuild:
+ sci-biology/cgview-bin: fixed installation of perl-related files
+
18 Feb 2015; Justin Lecher <jlec@gentoo.org> cgview-bin-20131130.ebuild:
sci-biology/cgview-bin: fix SLOT operators; drop KEYWORDS as fetch failed
diff --git a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild
index 61141e3..74a9540 100644
--- a/sci-biology/cgview-bin/cgview-bin-20131130.ebuild
+++ b/sci-biology/cgview-bin/cgview-bin-20131130.ebuild
@@ -6,6 +6,9 @@ EAPI=5
inherit java-pkg-2
+PERL_EXPORT_PHASE_FUNCTIONS=no
+inherit perl-module eutils toolchain-funcs
+
DESCRIPTION="CGView Comparison Tool to compare genome sequences graphically (aka CCT)"
HOMEPAGE="http://stothard.afns.ualberta.ca/downloads/CCT"
SRC_URI="http://www.ualberta.ca/~stothard/downloads/cgview_comparison_tool.zip"
@@ -34,11 +37,16 @@ src_test(){
}
src_install() {
- echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview_comparison_tool' > "${S}/99cgview"
+ insinto /usr/share/${PN}/scripts
+ chmod a+x scripts/* # BUG: this does not work
+ doins scripts/*
+ echo 'CCT_HOME='${EPREFIX}'/usr/share/cgview' > "${S}/99cgview"
echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview"
doenvd "${S}/99cgview"
- #export PATH="$PATH":"${CCT_HOME}/scripts":/path/to/blast-2.2.25/bin
- #export PERL5LIB="${CCT_HOME}"/lib/bioperl-1.2.3:"${CCT_HOME}"/lib/perl_modules:"$PERL5LIB"
-
- dobin bin/cgview.jar
+ perl_set_version
+ insinto ${VENDOR_LIB}/cgview
+ doins lib/perl_modules/Util/*.pm
+ #
+ # Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2DIOException
+ java-pkg_dojar bin/cgview.jar
}
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/cgview-bin/
@ 2021-03-18 18:54 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2021-03-18 18:54 UTC (permalink / raw
To: gentoo-commits
commit: 7cdc60382f8bf83952e639c8c6001f23eab7738d
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Thu Mar 18 18:39:05 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Thu Mar 18 18:39:05 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7cdc6038
sci-biology/cgview-bin: use perl_domodule
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild | 3 +--
1 file changed, 1 insertion(+), 2 deletions(-)
diff --git a/sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild b/sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild
index 2d1f4103b..5135e04ab 100644
--- a/sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild
+++ b/sci-biology/cgview-bin/cgview-bin-1.0.0.ebuild
@@ -36,8 +36,7 @@ src_install() {
echo 'PATH="$PATH":"'${CCT_HOME}'/scripts"' >> "${S}/99cgview"
doenvd "${S}/99cgview"
perl_set_version
- insinto ${VENDOR_LIB}/cgview
- doins lib/perl_modules/Util/*.pm
+ perl_domodule lib/perl_modules/Util/*.pm
#
# Exception in thread "main" java.lang.NoClassDefFoundError: org/apache/batik/svggen/SVGGraphics2DIOException
java-pkg_dojar bin/cgview/cgview.jar
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