trimmomatic: Flexible read trimming tool for Illumina NGS data

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Sep 14 15:40:59 2018 -0500
Changeset:	c2d7de61682a2ebd8a53d5e36721f6d34349a99f

Modified Files:
	Makefile
Added Files:
	trimmomatic/DESCR
	trimmomatic/Makefile
	trimmomatic/PLIST
	trimmomatic/distinfo

Log Message:
trimmomatic: Flexible read trimming tool for Illumina NGS data

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=c2d7de61682a2ebd8a53d5e36721f6d34349a99f

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

diffstat:
 Makefile             |  1 +
 trimmomatic/DESCR    |  2 ++
 trimmomatic/Makefile | 34 ++++++++++++++++++++++++++++++++++
 trimmomatic/PLIST    |  8 ++++++++
 trimmomatic/distinfo |  6 ++++++
 5 files changed, 51 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 2b5d72c92b..ced22360b2 100644
--- a/Makefile
+++ b/Makefile
@@ -4441,6 +4441,7 @@ SUBDIR+=	trelby
 SUBDIR+=	triangle
 SUBDIR+=	triforce-afl
 SUBDIR+=	trimadap
+SUBDIR+=	trimmomatic
 SUBDIR+=	trinity
 SUBDIR+=	tripwire2
 SUBDIR+=	truecrypt
diff --git a/trimmomatic/DESCR b/trimmomatic/DESCR
new file mode 100644
index 0000000000..acf81906fa
--- /dev/null
+++ b/trimmomatic/DESCR
@@ -0,0 +1,2 @@
+Trimmomatic performs a variety of useful trimming tasks for illumina
+NGS paired-end and single ended data.
diff --git a/trimmomatic/Makefile b/trimmomatic/Makefile
new file mode 100644
index 0000000000..39cc126b21
--- /dev/null
+++ b/trimmomatic/Makefile
@@ -0,0 +1,34 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Fri Sep 14 15:34:17 CDT 2018               #
+###########################################################
+
+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_LANGUAGES=	c c++
+USE_TOOLS+=	pax
+USE_JAVA=	run
+NO_BUILD=	yes
+
+PV=		0.38
+DATADIR=	${PREFIX}/share/trimmomatic
+JAVAJARDIR=	${PREFIX}/share/java/classes
+
+INSTALLATION_DIRS=	share/trimmomatic share/java/classes
+
+do-install:
+	${INSTALL_DATA} ${WRKSRC}/trimmomatic-${PV}.jar \
+		${DESTDIR}${JAVAJARDIR}/trimmomatic.jar
+	cd ${WRKSRC} && pax -rw adapters ${DESTDIR}${DATADIR}
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/trimmomatic/PLIST b/trimmomatic/PLIST
new file mode 100644
index 0000000000..68225577e0
--- /dev/null
+++ b/trimmomatic/PLIST
@@ -0,0 +1,8 @@
+@comment $NetBSD$
+share/java/classes/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/trimmomatic/distinfo b/trimmomatic/distinfo
new file mode 100644
index 0000000000..e7f63d90b0
--- /dev/null
+++ b/trimmomatic/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+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