trimmomatic: Remove, committed to biology

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

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Wed Jul 25 15:12:29 2018 -0500
Changeset:	f450fc950c23eef7b4b95d8d732fe1349af601bf

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

Log Message:
trimmomatic: Remove, committed to biology

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f450fc950c23eef7b4b95d8d732fe1349af601bf

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

diffstat:
 Makefile             |  1 -
 trimmomatic/DESCR    |  5 -----
 trimmomatic/Makefile | 28 ----------------------------
 trimmomatic/PLIST    |  8 --------
 trimmomatic/distinfo |  6 ------
 5 files changed, 48 deletions(-)

diffs:
diff --git a/Makefile b/Makefile
index 9438a516d9..8e4911435c 100644
--- a/Makefile
+++ b/Makefile
@@ -4455,7 +4455,6 @@ 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
deleted file mode 100644
index 597bd8a434..0000000000
--- a/trimmomatic/DESCR
+++ /dev/null
@@ -1,5 +0,0 @@
-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/trimmomatic/Makefile b/trimmomatic/Makefile
deleted file mode 100644
index 785a89a1d5..0000000000
--- a/trimmomatic/Makefile
+++ /dev/null
@@ -1,28 +0,0 @@
-# $NetBSD$
-
-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"
diff --git a/trimmomatic/PLIST b/trimmomatic/PLIST
deleted file mode 100644
index 9f5570021a..0000000000
--- a/trimmomatic/PLIST
+++ /dev/null
@@ -1,8 +0,0 @@
-@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/distinfo b/trimmomatic/distinfo
deleted file mode 100644
index e7f63d90b0..0000000000
--- a/trimmomatic/distinfo
+++ /dev/null
@@ -1,6 +0,0 @@
-$NetBSD$
-
-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