diff options
| author | bacon <bacon@pkgsrc.org> | 2018-07-25 15:14:32 +0000 |
|---|---|---|
| committer | bacon <bacon@pkgsrc.org> | 2018-07-25 15:14:32 +0000 |
| commit | 4964d24303a4b7b4ec372b6fde4a11b4226e791c (patch) | |
| tree | 5e2be367ea2fe028c5751aa4d942a81a97e611d6 /biology | |
| parent | bbb97402c3cf08d55799d9cb2b376bdae5154db8 (diff) | |
| download | pkgsrc-4964d24303a4b7b4ec372b6fde4a11b4226e791c.tar.gz | |
biology/trimmomatic: import Trimmomatic-0.38
Trimmomatic performs a variety of useful trimming tasks for illumina
paired-end and single ended data. The selection of trimming steps and their
associated parameters are supplied on the command line. It works with FASTQ
(using phred + 33 or phred + 64 quality scores, depending on the Illumina
pipeline used), either uncompressed or gzipp'ed FASTQ.
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/trimmomatic/DESCR | 5 | ||||
| -rw-r--r-- | biology/trimmomatic/Makefile | 28 | ||||
| -rw-r--r-- | biology/trimmomatic/PLIST | 8 | ||||
| -rw-r--r-- | biology/trimmomatic/distinfo | 6 |
4 files changed, 47 insertions, 0 deletions
diff --git a/biology/trimmomatic/DESCR b/biology/trimmomatic/DESCR new file mode 100644 index 00000000000..597bd8a434a --- /dev/null +++ b/biology/trimmomatic/DESCR @@ -0,0 +1,5 @@ +Trimmomatic performs a variety of useful trimming tasks for illumina +paired-end and single ended data. The selection of trimming steps and their +associated parameters are supplied on the command line. It works with FASTQ +(using phred + 33 or phred + 64 quality scores, depending on the Illumina +pipeline used), either uncompressed or gzipp'ed FASTQ. diff --git a/biology/trimmomatic/Makefile b/biology/trimmomatic/Makefile new file mode 100644 index 00000000000..9faa55877c3 --- /dev/null +++ b/biology/trimmomatic/Makefile @@ -0,0 +1,28 @@ +# $NetBSD: Makefile,v 1.1 2018/07/25 15:14:32 bacon Exp $ + +DISTNAME= Trimmomatic-${PV} +CATEGORIES= biology +MASTER_SITES= http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/ +EXTRACT_SUFX= .zip + +MAINTAINER= bacon@NetBSD.org +HOMEPAGE= http://www.usadellab.org/cms/?page=trimmomatic +COMMENT= Flexible read trimming tool for Illumina NGS data +LICENSE= gnu-gpl-v3 + +USE_TOOLS+= pax +USE_JAVA= run +NO_BUILD= yes + +WRKSRC= ${WRKDIR}/Trimmomatic-${PV} + +INSTALLATION_DIRS= lib/java share/trimmomatic + +PV= 0.38 + +do-install: + ${INSTALL_DATA} ${WRKSRC}/trimmomatic-${PV}.jar \ + ${DESTDIR}${PREFIX}/lib/java/trimmomatic.jar + cd ${WRKSRC} && pax -rw adapters ${DESTDIR}${PREFIX}/share/trimmomatic + +.include "../../mk/bsd.pkg.mk" diff --git a/biology/trimmomatic/PLIST b/biology/trimmomatic/PLIST new file mode 100644 index 00000000000..f0238056ec7 --- /dev/null +++ b/biology/trimmomatic/PLIST @@ -0,0 +1,8 @@ +@comment $NetBSD: PLIST,v 1.1 2018/07/25 15:14:32 bacon Exp $ +lib/java/trimmomatic.jar +share/trimmomatic/adapters/NexteraPE-PE.fa +share/trimmomatic/adapters/TruSeq2-PE.fa +share/trimmomatic/adapters/TruSeq2-SE.fa +share/trimmomatic/adapters/TruSeq3-PE-2.fa +share/trimmomatic/adapters/TruSeq3-PE.fa +share/trimmomatic/adapters/TruSeq3-SE.fa diff --git a/biology/trimmomatic/distinfo b/biology/trimmomatic/distinfo new file mode 100644 index 00000000000..5f7f877d0b4 --- /dev/null +++ b/biology/trimmomatic/distinfo @@ -0,0 +1,6 @@ +$NetBSD: distinfo,v 1.1 2018/07/25 15:14:32 bacon Exp $ + +SHA1 (Trimmomatic-0.38.zip) = e255b1f6c53a97e1c09c0ca6327b1798d3a36e78 +RMD160 (Trimmomatic-0.38.zip) = 8fbb1b03928c21dd637973ec10e28a107e800e54 +SHA512 (Trimmomatic-0.38.zip) = 899807a091e491a4f99c1522f9db52d7563da891393a9f20aa19c504be55956d8309564e8cca46bc3e956a4d9602d5c9475f3a1e622a501b6920aa3f3f72743b +Size (Trimmomatic-0.38.zip) = 132647 bytes |