Import Trimmomatic-0.35 as wip/trimmomatic.

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed May 11 07:32:34 2016 -0500
Changeset:	b0d08cd60b0e9a6c1fd989e6b8a4a9cfc8a14b5b

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

Log Message:
Import Trimmomatic-0.35 as wip/trimmomatic.

A 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=b0d08cd60b0e9a6c1fd989e6b8a4a9cfc8a14b5b

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

diffstat:
 trimmomatic/DESCR    |  1 +
 trimmomatic/Makefile | 35 +++++++++++++++++++++++++++++++++++
 trimmomatic/PLIST    |  8 ++++++++
 trimmomatic/TODO     |  1 +
 trimmomatic/distinfo |  5 +++++
 5 files changed, 50 insertions(+)

diffs:
diff --git a/trimmomatic/DESCR b/trimmomatic/DESCR
new file mode 100644
index 0000000..e55145a
--- /dev/null
+++ b/trimmomatic/DESCR
@@ -0,0 +1 @@
+A flexible read trimming tool for Illumina NGS data
diff --git a/trimmomatic/Makefile b/trimmomatic/Makefile
new file mode 100644
index 0000000..59be13d
--- /dev/null
+++ b/trimmomatic/Makefile
@@ -0,0 +1,35 @@
+# $NetBSD$
+#
+###########################################################
+#               Generated by fbsd2pkg                     #
+###########################################################
+
+DISTNAME=	Trimmomatic-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/
+EXTRACT_SUFX=	.zip
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	http://www.usadellab.org/cms/?page=trimmomatic
+COMMENT=	Flexible read trimming tool for Illumina NGS data
+LICENSE=	gnu-gpl-v3
+
+# Use Yum's java for now
+# USE_JAVA=	run
+
+# Just assuming C and C++: Adjust this!
+USE_TOOLS+=	pax
+NO_BUILD=	yes
+
+WRKSRC=		${WRKDIR}/Trimmomatic-${PORTVERSION}
+
+PORTVERSION=	0.35
+DATADIR=	${PREFIX}/share/Trimmomatic
+
+INSTALLATION_DIRS=	bin lib/java share/Trimmomatic
+
+do-install:
+	${INSTALL_DATA} ${WRKSRC}/trimmomatic-0.35.jar ${DESTDIR}${PREFIX}/lib/java/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 0000000..f100a6c
--- /dev/null
+++ b/trimmomatic/PLIST
@@ -0,0 +1,8 @@
+@comment $NetBSD$
+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/trimmomatic/TODO b/trimmomatic/TODO
new file mode 100644
index 0000000..b2e3b56
--- /dev/null
+++ b/trimmomatic/TODO
@@ -0,0 +1 @@
+Clean up and test.
diff --git a/trimmomatic/distinfo b/trimmomatic/distinfo
new file mode 100644
index 0000000..d759b21
--- /dev/null
+++ b/trimmomatic/distinfo
@@ -0,0 +1,5 @@
+$NetBSD$
+
+SHA1 (Trimmomatic-0.35.zip) = e0bb6fe765729ed9eb78e83b4d7fd734feff9f72
+RMD160 (Trimmomatic-0.35.zip) = 528d11d297e6f49df5eefb83a838db0e9da17059
+Size (Trimmomatic-0.35.zip) = 129810 bytes