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Import Trimmomatic-0.35 as wip/trimmomatic.
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
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