svn commit: r411261 - in head/biology: . trimmomatic
Wen Heping
wen at FreeBSD.org
Thu Mar 17 08:21:16 UTC 2016
Author: wen
Date: Thu Mar 17 08:21:14 2016
New Revision: 411261
URL: https://svnweb.freebsd.org/changeset/ports/411261
Log:
Trimmomatic performs a variety of useful trimming tasks for illumina
NGS paired-end and single ended data.
WWW: http://www.usadellab.org/cms/?page=trimmomatic
PR: 208044
Submitted by: bacon4000 at gmail.com
Added:
head/biology/trimmomatic/
head/biology/trimmomatic/Makefile (contents, props changed)
head/biology/trimmomatic/distinfo (contents, props changed)
head/biology/trimmomatic/pkg-descr (contents, props changed)
head/biology/trimmomatic/pkg-plist (contents, props changed)
Modified:
head/biology/Makefile
Modified: head/biology/Makefile
==============================================================================
--- head/biology/Makefile Thu Mar 17 07:03:42 2016 (r411260)
+++ head/biology/Makefile Thu Mar 17 08:21:14 2016 (r411261)
@@ -95,6 +95,7 @@
SUBDIR += tinker
SUBDIR += treepuzzle
SUBDIR += treeviewx
+ SUBDIR += trimmomatic
SUBDIR += ugene
SUBDIR += vcftools
SUBDIR += velvet
Added: head/biology/trimmomatic/Makefile
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/trimmomatic/Makefile Thu Mar 17 08:21:14 2016 (r411261)
@@ -0,0 +1,27 @@
+# Created by: Dan Siercks <dsiercks at uwm.edu>
+# $FreeBSD$
+
+PORTNAME= trimmomatic
+PORTVERSION= 0.35
+CATEGORIES= biology java
+MASTER_SITES= http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/
+DISTNAME= Trimmomatic-${PORTVERSION}
+
+MAINTAINER= bacon4000 at gmail.com
+COMMENT= Flexible read trimming tool for Illumina NGS data
+
+LICENSE= GPLv3
+
+USES= zip
+USE_JAVA= yes
+JAVA_VERSION= 1.6+
+JAVA_RUN= yes
+NO_BUILD= yes
+NO_ARCH= yes
+
+do-install:
+ ${INSTALL_DATA} ${WRKSRC}/trimmomatic-${PORTVERSION}.jar \
+ ${STAGEDIR}${JAVAJARDIR}/trimmomatic.jar
+ cd ${WRKSRC} && ${COPYTREE_SHARE} adapters ${STAGEDIR}${DATADIR}
+
+.include <bsd.port.mk>
Added: head/biology/trimmomatic/distinfo
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/trimmomatic/distinfo Thu Mar 17 08:21:14 2016 (r411261)
@@ -0,0 +1,2 @@
+SHA256 (Trimmomatic-0.35.zip) = 43b993ffa91c039b529db8334bc6aa4b0d601e69c79aaa9a1457ecd1c2c3cc69
+SIZE (Trimmomatic-0.35.zip) = 129810
Added: head/biology/trimmomatic/pkg-descr
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/trimmomatic/pkg-descr Thu Mar 17 08:21:14 2016 (r411261)
@@ -0,0 +1,4 @@
+Trimmomatic performs a variety of useful trimming tasks for illumina
+NGS paired-end and single ended data.
+
+WWW: http://www.usadellab.org/cms/?page=trimmomatic
Added: head/biology/trimmomatic/pkg-plist
==============================================================================
--- /dev/null 00:00:00 1970 (empty, because file is newly added)
+++ head/biology/trimmomatic/pkg-plist Thu Mar 17 08:21:14 2016 (r411261)
@@ -0,0 +1,7 @@
+%%DATADIR%%/adapters/NexteraPE-PE.fa
+%%DATADIR%%/adapters/TruSeq2-PE.fa
+%%DATADIR%%/adapters/TruSeq2-SE.fa
+%%DATADIR%%/adapters/TruSeq3-PE-2.fa
+%%DATADIR%%/adapters/TruSeq3-PE.fa
+%%DATADIR%%/adapters/TruSeq3-SE.fa
+%%JAVAJARDIR%%/trimmomatic.jar
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