trimmomatic: Clean up

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Jul 5 09:48:17 2018 -0500
Changeset:	8d8a9743e396bc606ec04ce4844a0b56d9de8b40

Modified Files:
	trimmomatic/DESCR
	trimmomatic/Makefile
	trimmomatic/distinfo
Removed Files:
	trimmomatic/TODO

Log Message:
trimmomatic: Clean up

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=8d8a9743e396bc606ec04ce4844a0b56d9de8b40

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

diffstat:
 trimmomatic/DESCR    |  7 ++++++-
 trimmomatic/Makefile | 18 ++++++++----------
 trimmomatic/TODO     |  1 -
 trimmomatic/distinfo |  8 ++++----
 4 files changed, 18 insertions(+), 16 deletions(-)

diffs:
diff --git a/trimmomatic/DESCR b/trimmomatic/DESCR
index e55145a25b..79ad3f95ac 100644
--- a/trimmomatic/DESCR
+++ b/trimmomatic/DESCR
@@ -1 +1,6 @@
-A flexible read trimming tool for Illumina NGS data
+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. Use of gzip format
+is determined based on the .gz extension.
diff --git a/trimmomatic/Makefile b/trimmomatic/Makefile
index 382ac4e9a7..785a89a1d5 100644
--- a/trimmomatic/Makefile
+++ b/trimmomatic/Makefile
@@ -1,6 +1,6 @@
 # $NetBSD$
 
-DISTNAME=	Trimmomatic-${PORTVERSION}
+DISTNAME=	Trimmomatic-${PV}
 CATEGORIES=	biology
 MASTER_SITES=	http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/
 EXTRACT_SUFX=	.zip
@@ -10,21 +10,19 @@ HOMEPAGE=	http://www.usadellab.org/cms/?page=trimmomatic
 COMMENT=	Flexible read trimming tool for Illumina NGS data
 LICENSE=	gnu-gpl-v3
 
-# FIXME: Should at least error out if no jvm available on Linux
-USE_JAVA=	run
-
 USE_TOOLS+=	pax
+USE_JAVA=	run
 NO_BUILD=	yes
 
-WRKSRC=		${WRKDIR}/Trimmomatic-${PORTVERSION}
-
-PORTVERSION=	0.35
-DATADIR=	${PREFIX}/share/trimmomatic
+WRKSRC=		${WRKDIR}/Trimmomatic-${PV}
 
 INSTALLATION_DIRS=	lib/java share/trimmomatic
 
+PV=		0.38
+
 do-install:
-	${INSTALL_DATA} ${WRKSRC}/trimmomatic-0.35.jar ${DESTDIR}${PREFIX}/lib/java/trimmomatic.jar
-	cd ${WRKSRC} && pax -rw adapters ${DESTDIR}${DATADIR}
+	${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/trimmomatic/TODO b/trimmomatic/TODO
deleted file mode 100644
index b2e3b56f25..0000000000
--- a/trimmomatic/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test.
diff --git a/trimmomatic/distinfo b/trimmomatic/distinfo
index 4d57662a12..e7f63d90b0 100644
--- a/trimmomatic/distinfo
+++ b/trimmomatic/distinfo
@@ -1,6 +1,6 @@
 $NetBSD$
 
-SHA1 (Trimmomatic-0.35.zip) = e0bb6fe765729ed9eb78e83b4d7fd734feff9f72
-RMD160 (Trimmomatic-0.35.zip) = 528d11d297e6f49df5eefb83a838db0e9da17059
-SHA512 (Trimmomatic-0.35.zip) = 45eeae2480208ed21b8106c37ad708e007bd16fb92f7b5a069d7feb5c60e5dbf4f3b6713709ec306cc11ced645c3925627a3fc0ecf4181e9539be75b29476453
-Size (Trimmomatic-0.35.zip) = 129810 bytes
+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