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| author | wen <wen@FreeBSD.org> | 2016-03-17 16:21:14 +0800 |
|---|---|---|
| committer | wen <wen@FreeBSD.org> | 2016-03-17 16:21:14 +0800 |
| commit | 27b94b50a7865d69c6c14f6c102f8e7af275ec20 (patch) | |
| tree | e0615b8e204e8dd3bb4a82e004d5ecb77111ce29 /biology | |
| parent | 910e03ab0815fb0963265b0a140a62f51057ca3d (diff) | |
| download | freebsd-ports-gnome-27b94b50a7865d69c6c14f6c102f8e7af275ec20.tar.gz freebsd-ports-gnome-27b94b50a7865d69c6c14f6c102f8e7af275ec20.tar.zst freebsd-ports-gnome-27b94b50a7865d69c6c14f6c102f8e7af275ec20.zip | |
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@gmail.com
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/Makefile | 1 | ||||
| -rw-r--r-- | biology/trimmomatic/Makefile | 27 | ||||
| -rw-r--r-- | biology/trimmomatic/distinfo | 2 | ||||
| -rw-r--r-- | biology/trimmomatic/pkg-descr | 4 | ||||
| -rw-r--r-- | biology/trimmomatic/pkg-plist | 7 |
5 files changed, 41 insertions, 0 deletions
diff --git a/biology/Makefile b/biology/Makefile index 08458a335d1c..b998d56847ca 100644 --- a/biology/Makefile +++ b/biology/Makefile @@ -95,6 +95,7 @@ SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += treeviewx + SUBDIR += trimmomatic SUBDIR += ugene SUBDIR += vcftools SUBDIR += velvet diff --git a/biology/trimmomatic/Makefile b/biology/trimmomatic/Makefile new file mode 100644 index 000000000000..50c881595d83 --- /dev/null +++ b/biology/trimmomatic/Makefile @@ -0,0 +1,27 @@ +# Created by: Dan Siercks <dsiercks@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@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> diff --git a/biology/trimmomatic/distinfo b/biology/trimmomatic/distinfo new file mode 100644 index 000000000000..fc50ab760f76 --- /dev/null +++ b/biology/trimmomatic/distinfo @@ -0,0 +1,2 @@ +SHA256 (Trimmomatic-0.35.zip) = 43b993ffa91c039b529db8334bc6aa4b0d601e69c79aaa9a1457ecd1c2c3cc69 +SIZE (Trimmomatic-0.35.zip) = 129810 diff --git a/biology/trimmomatic/pkg-descr b/biology/trimmomatic/pkg-descr new file mode 100644 index 000000000000..48c589bd5abd --- /dev/null +++ b/biology/trimmomatic/pkg-descr @@ -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 diff --git a/biology/trimmomatic/pkg-plist b/biology/trimmomatic/pkg-plist new file mode 100644 index 000000000000..be4315845557 --- /dev/null +++ b/biology/trimmomatic/pkg-plist @@ -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 |