CVS commit: pkgsrc/biology/trimmomatic

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Wed Jul 25 15:14:32 UTC 2018

Added Files:
        pkgsrc/biology/trimmomatic: DESCR Makefile PLIST distinfo

Log Message:
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.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/trimmomatic/DESCR \
    pkgsrc/biology/trimmomatic/Makefile pkgsrc/biology/trimmomatic/PLIST \
    pkgsrc/biology/trimmomatic/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/biology/trimmomatic/DESCR
diff -u /dev/null pkgsrc/biology/trimmomatic/DESCR:1.1
--- /dev/null   Wed Jul 25 15:14:32 2018
+++ pkgsrc/biology/trimmomatic/DESCR    Wed Jul 25 15:14:32 2018
@@ -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.
Index: pkgsrc/biology/trimmomatic/Makefile
diff -u /dev/null pkgsrc/biology/trimmomatic/Makefile:1.1
--- /dev/null   Wed Jul 25 15:14:32 2018
+++ pkgsrc/biology/trimmomatic/Makefile Wed Jul 25 15:14:32 2018
@@ -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@localhost
+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"
Index: pkgsrc/biology/trimmomatic/PLIST
diff -u /dev/null pkgsrc/biology/trimmomatic/PLIST:1.1
--- /dev/null   Wed Jul 25 15:14:32 2018
+++ pkgsrc/biology/trimmomatic/PLIST    Wed Jul 25 15:14:32 2018
@@ -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
Index: pkgsrc/biology/trimmomatic/distinfo
diff -u /dev/null pkgsrc/biology/trimmomatic/distinfo:1.1
--- /dev/null   Wed Jul 25 15:14:32 2018
+++ pkgsrc/biology/trimmomatic/distinfo Wed Jul 25 15:14:32 2018
@@ -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