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biology/trimmomatic: Upgrade to 0.39

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Add convenience script to run without knowing the location of the Java jar
This commit is contained in:
Jason W. Bacon 2019-09-14 14:45:49 +00:00
parent 63008e23ae
commit 848c6ffeb5
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=512018
4 changed files with 14 additions and 4 deletions
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7
biology/trimmomatic/Makefile
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@ -2,7 +2,7 @@
# $FreeBSD$
PORTNAME= trimmomatic
PORTVERSION= 0.35
DISTVERSION= 0.39
CATEGORIES= biology java
MASTER_SITES= http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/
DISTNAME= Trimmomatic-${PORTVERSION}
@ -11,17 +11,22 @@ MAINTAINER= jwb@FreeBSD.org
COMMENT= Flexible read trimming tool for Illumina NGS data
LICENSE= GPLv3
LICENSE_FILE= ${WRKSRC}/LICENSE
USES= zip
USE_JAVA= yes
JAVA_VERSION= 1.6+
JAVA_RUN= yes
NO_BUILD= yes
NO_ARCH= yes
SUB_FILES= trimmomatic
do-install:
${INSTALL_DATA} ${WRKSRC}/trimmomatic-${PORTVERSION}.jar \
${STAGEDIR}${JAVAJARDIR}/trimmomatic.jar
cd ${WRKSRC} && ${COPYTREE_SHARE} adapters ${STAGEDIR}${DATADIR}
${INSTALL_SCRIPT} ${WRKDIR}/trimmomatic ${STAGEDIR}${PREFIX}/bin
.include <bsd.port.mk>

5
biology/trimmomatic/distinfo
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@ -1,2 +1,3 @@
SHA256 (Trimmomatic-0.35.zip) = 43b993ffa91c039b529db8334bc6aa4b0d601e69c79aaa9a1457ecd1c2c3cc69
SIZE (Trimmomatic-0.35.zip) = 129810
TIMESTAMP = 1568469691
SHA256 (Trimmomatic-0.39.zip) = 2f97e3a237378d55c221abfc38e4b11ea232c8a41d511b8b4871f00c0476abca
SIZE (Trimmomatic-0.39.zip) = 133596

3
biology/trimmomatic/files/trimmomatic.in Normal file
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@ -0,0 +1,3 @@
#!/bin/sh -e
java -jar %%PREFIX%%/share/java/classes/trimmomatic.jar "$@"

3
biology/trimmomatic/pkg-plist
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@ -1,7 +1,8 @@
bin/trimmomatic
%%JAVAJARDIR%%/trimmomatic.jar
%%DATADIR%%/adapters/NexteraPE-PE.fa
%%DATADIR%%/adapters/TruSeq2-PE.fa
%%DATADIR%%/adapters/TruSeq2-SE.fa
%%DATADIR%%/adapters/TruSeq3-PE-2.fa
%%DATADIR%%/adapters/TruSeq3-PE.fa
%%DATADIR%%/adapters/TruSeq3-SE.fa
%%JAVAJARDIR%%/trimmomatic.jar