* [gentoo-commits] proj/sci:master commit in: sci-biology/trimmomatic/
@ 2015-01-22 21:47 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2015-01-22 21:47 UTC (permalink / raw
To: gentoo-commits
commit: 43383a65794cbfd08269dbaea69a67d7787479d8
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Jan 22 21:45:58 2015 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Jan 22 21:45:58 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=43383a65
sci-biology/trimmomatic: new package
Package-Manager: portage-2.2.15
---
sci-biology/trimmomatic/ChangeLog | 9 +++++++
sci-biology/trimmomatic/metadata.xml | 9 +++++++
sci-biology/trimmomatic/trimmomatic-0.32.ebuild | 36 +++++++++++++++++++++++++
3 files changed, 54 insertions(+)
diff --git a/sci-biology/trimmomatic/ChangeLog b/sci-biology/trimmomatic/ChangeLog
new file mode 100644
index 0000000..119ca3f
--- /dev/null
+++ b/sci-biology/trimmomatic/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/trimmomatic
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*trimmomatic-0.32 (22 Jan 2015)
+
+ 22 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
+ +trimmomatic-0.32.ebuild:
+ sci-biology/trimmomatic: new package
diff --git a/sci-biology/trimmomatic/metadata.xml b/sci-biology/trimmomatic/metadata.xml
new file mode 100644
index 0000000..2bc8930
--- /dev/null
+++ b/sci-biology/trimmomatic/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>
diff --git a/sci-biology/trimmomatic/trimmomatic-0.32.ebuild b/sci-biology/trimmomatic/trimmomatic-0.32.ebuild
new file mode 100644
index 0000000..662ceea
--- /dev/null
+++ b/sci-biology/trimmomatic/trimmomatic-0.32.ebuild
@@ -0,0 +1,36 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+inherit java-pkg-2 java-ant-2
+
+DESCRIPTION="Illumina adapter trimming tool"
+HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic"
+SRC_URI="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-0.32.zip
+ http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf -> "${P}"_manual.pdf"
+
+# http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND=">=virtual/jdk-1.6
+ dev-java/ant-core"
+RDEPEND="${DEPEND}
+ >=virtual/jre-1.6"
+
+# somehow fails to build with oracle-jdk-bin-1.7 while ibm-jdk-bin-1.6 works
+
+EANT_BUILD_TARGET="dist"
+
+src_install() {
+ java-pkg_newjar "dist/jar/${P}.jar" "${PN}.jar"
+ insinto /usr/share/"${PN}"/Illumina
+ doins adapters/*.fa
+ insinto /usr/share/doc/"${P}"
+ dodoc "${DISTDIR}"/"${P}"_manual.pdf
+}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/trimmomatic/
@ 2015-02-18 16:41 Justin Lecher
0 siblings, 0 replies; 7+ messages in thread
From: Justin Lecher @ 2015-02-18 16:41 UTC (permalink / raw
To: gentoo-commits
commit: fea9570c8c2206218e474d15d0637d1ac95c9311
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Feb 18 13:45:40 2015 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Feb 18 13:45:40 2015 +0000
URL: http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=fea9570c
sci-biology/trimmomatic: fix SLOT operators
Package-Manager: portage-2.2.17
---
sci-biology/trimmomatic/ChangeLog | 3 +++
sci-biology/trimmomatic/trimmomatic-0.32.ebuild | 14 +++++++-------
2 files changed, 10 insertions(+), 7 deletions(-)
diff --git a/sci-biology/trimmomatic/ChangeLog b/sci-biology/trimmomatic/ChangeLog
index 119ca3f..010e50b 100644
--- a/sci-biology/trimmomatic/ChangeLog
+++ b/sci-biology/trimmomatic/ChangeLog
@@ -2,6 +2,9 @@
# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Feb 2015; Justin Lecher <jlec@gentoo.org> trimmomatic-0.32.ebuild:
+ sci-biology/trimmomatic: fix SLOT operators
+
*trimmomatic-0.32 (22 Jan 2015)
22 Jan 2015; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz> +metadata.xml,
diff --git a/sci-biology/trimmomatic/trimmomatic-0.32.ebuild b/sci-biology/trimmomatic/trimmomatic-0.32.ebuild
index 662ceea..c29b9c0 100644
--- a/sci-biology/trimmomatic/trimmomatic-0.32.ebuild
+++ b/sci-biology/trimmomatic/trimmomatic-0.32.ebuild
@@ -8,7 +8,8 @@ inherit java-pkg-2 java-ant-2
DESCRIPTION="Illumina adapter trimming tool"
HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic"
-SRC_URI="http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-0.32.zip
+SRC_URI="
+ http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-0.32.zip
http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf -> "${P}"_manual.pdf"
# http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
@@ -18,10 +19,9 @@ SLOT="0"
KEYWORDS="~amd64"
IUSE=""
-DEPEND=">=virtual/jdk-1.6
+DEPEND=">=virtual/jdk-1.6:*
dev-java/ant-core"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.6"
+RDEPEND=">=virtual/jre-1.6:*"
# somehow fails to build with oracle-jdk-bin-1.7 while ibm-jdk-bin-1.6 works
@@ -29,8 +29,8 @@ EANT_BUILD_TARGET="dist"
src_install() {
java-pkg_newjar "dist/jar/${P}.jar" "${PN}.jar"
- insinto /usr/share/"${PN}"/Illumina
+ insinto /usr/share/${PN}/Illumina
doins adapters/*.fa
- insinto /usr/share/doc/"${P}"
- dodoc "${DISTDIR}"/"${P}"_manual.pdf
+ insinto /usr/share/doc/${P}
+ dodoc "${DISTDIR}"/${P}_manual.pdf
}
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/trimmomatic/
@ 2016-03-15 13:07 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2016-03-15 13:07 UTC (permalink / raw
To: gentoo-commits
commit: 83c16a81e098d57b8ce33eaa7900facebc0c6b3c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 15 13:03:20 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 15 13:03:20 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=83c16a81
sci-biology/trimmomatic: version bump; no 0.35 PDF manual exists for download
Package-Manager: portage-2.2.26
.../trimmomatic/{trimmomatic-0.32.ebuild => trimmomatic-0.35.ebuild} | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/sci-biology/trimmomatic/trimmomatic-0.32.ebuild b/sci-biology/trimmomatic/trimmomatic-0.35.ebuild
similarity index 97%
rename from sci-biology/trimmomatic/trimmomatic-0.32.ebuild
rename to sci-biology/trimmomatic/trimmomatic-0.35.ebuild
index 748c293..729b90f 100644
--- a/sci-biology/trimmomatic/trimmomatic-0.32.ebuild
+++ b/sci-biology/trimmomatic/trimmomatic-0.35.ebuild
@@ -9,7 +9,7 @@ inherit java-pkg-2 java-ant-2
DESCRIPTION="Illumina adapter trimming tool"
HOMEPAGE="http://www.usadellab.org/cms/?page=trimmomatic"
SRC_URI="
- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-0.32.zip
+ http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-Src-${PV}.zip
http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/TrimmomaticManual_V0.32.pdf -> "${P}"_manual.pdf"
# http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/trimmomatic/
@ 2017-03-22 14:33 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2017-03-22 14:33 UTC (permalink / raw
To: gentoo-commits
commit: 55fd9df6aa09d8646fee7b1adbb9f44012bb077d
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Mar 22 14:33:26 2017 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Mar 22 14:33:26 2017 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=55fd9df6
sci-biology/trimmomatic: version bump, bump to EAPI=6
Package-Manager: Portage-2.3.3, Repoman-2.3.1
.../trimmomatic/{trimmomatic-0.35.ebuild => trimmomatic-0.36.ebuild} | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/trimmomatic/trimmomatic-0.35.ebuild b/sci-biology/trimmomatic/trimmomatic-0.36.ebuild
similarity index 95%
rename from sci-biology/trimmomatic/trimmomatic-0.35.ebuild
rename to sci-biology/trimmomatic/trimmomatic-0.36.ebuild
index a602d1bf4..302a93af1 100644
--- a/sci-biology/trimmomatic/trimmomatic-0.35.ebuild
+++ b/sci-biology/trimmomatic/trimmomatic-0.36.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
-EAPI=5
+EAPI=6
inherit java-pkg-2 java-ant-2
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/trimmomatic/
@ 2018-06-06 8:09 Martin Mokrejs
0 siblings, 0 replies; 7+ messages in thread
From: Martin Mokrejs @ 2018-06-06 8:09 UTC (permalink / raw
To: gentoo-commits
commit: 42ce5293f70fbb7a48f81f1a30bf9ba2d029b6c1
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Jun 6 08:09:35 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Jun 6 08:09:35 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=42ce5293
sci-biology/trimmomatic: version bump
Package-Manager: Portage-2.3.40, Repoman-2.3.9
.../trimmomatic/{trimmomatic-0.36.ebuild => trimmomatic-0.38.ebuild} | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/sci-biology/trimmomatic/trimmomatic-0.36.ebuild b/sci-biology/trimmomatic/trimmomatic-0.38.ebuild
similarity index 93%
rename from sci-biology/trimmomatic/trimmomatic-0.36.ebuild
rename to sci-biology/trimmomatic/trimmomatic-0.38.ebuild
index 302a93af1..bf01fd874 100644
--- a/sci-biology/trimmomatic/trimmomatic-0.36.ebuild
+++ b/sci-biology/trimmomatic/trimmomatic-0.38.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -15,7 +15,7 @@ SRC_URI="
LICENSE="GPL-3"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND=">=virtual/jdk-1.6:*
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/trimmomatic/
@ 2021-01-19 16:56 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-01-19 16:56 UTC (permalink / raw
To: gentoo-commits
commit: 7aa650957b89af4260daa8e15b9938dc6cb48cce
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan 19 16:37:06 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan 19 16:37:06 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=7aa65095
sci-biology/trimmomatic: depend on unzip
Package-Manager: Portage-3.0.13, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
sci-biology/trimmomatic/trimmomatic-0.38.ebuild | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/sci-biology/trimmomatic/trimmomatic-0.38.ebuild b/sci-biology/trimmomatic/trimmomatic-0.38.ebuild
index bf01fd874..90995a52a 100644
--- a/sci-biology/trimmomatic/trimmomatic-0.38.ebuild
+++ b/sci-biology/trimmomatic/trimmomatic-0.38.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -19,7 +19,8 @@ KEYWORDS="~amd64 ~x86"
IUSE=""
DEPEND=">=virtual/jdk-1.6:*
- dev-java/ant-core"
+ dev-java/ant-core
+ app-arch/unzip"
RDEPEND=">=virtual/jre-1.6:*"
# somehow fails to build with oracle-jdk-bin-1.7 while ibm-jdk-bin-1.6 works
^ permalink raw reply related [flat|nested] 7+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/trimmomatic/
@ 2021-03-06 16:01 Andrew Ammerlaan
0 siblings, 0 replies; 7+ messages in thread
From: Andrew Ammerlaan @ 2021-03-06 16:01 UTC (permalink / raw
To: gentoo-commits
commit: 9e27cab74dc41bef630ef8ef63af65ffb6401ee9
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Sat Mar 6 15:42:38 2021 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Sat Mar 6 15:42:38 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=9e27cab7
sci-biology/trimmomatic: EAPI bump
Package-Manager: Portage-3.0.16, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
.../trimmomatic/{trimmomatic-0.38.ebuild => trimmomatic-0.39.ebuild} | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/sci-biology/trimmomatic/trimmomatic-0.38.ebuild b/sci-biology/trimmomatic/trimmomatic-0.39.ebuild
similarity index 95%
rename from sci-biology/trimmomatic/trimmomatic-0.38.ebuild
rename to sci-biology/trimmomatic/trimmomatic-0.39.ebuild
index 90995a52a..331ab5cd8 100644
--- a/sci-biology/trimmomatic/trimmomatic-0.38.ebuild
+++ b/sci-biology/trimmomatic/trimmomatic-0.39.ebuild
@@ -1,7 +1,7 @@
# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
inherit java-pkg-2 java-ant-2
@@ -16,7 +16,6 @@ SRC_URI="
LICENSE="GPL-3"
SLOT="0"
KEYWORDS="~amd64 ~x86"
-IUSE=""
DEPEND=">=virtual/jdk-1.6:*
dev-java/ant-core
@@ -31,6 +30,5 @@ src_install() {
java-pkg_newjar "dist/jar/${P}.jar" "${PN}.jar"
insinto /usr/share/${PN}/Illumina
doins adapters/*.fa
- insinto /usr/share/doc/${P}
dodoc "${DISTDIR}"/${P}_manual.pdf
}
^ permalink raw reply related [flat|nested] 7+ messages in thread
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