freebsd-ports/biology/trimmomatic/Makefile

PORTNAME=	trimmomatic
DISTVERSION=	0.39
CATEGORIES=	biology java
MASTER_SITES=	http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/
DISTNAME=	Trimmomatic-${PORTVERSION}

MAINTAINER=	jwb@FreeBSD.org
COMMENT=	Flexible read trimming tool for Illumina NGS data
WWW=		http://www.usadellab.org/cms/?page=trimmomatic

LICENSE=	GPLv3
LICENSE_FILE=	${WRKSRC}/LICENSE

USES=		zip
USE_JAVA=	yes

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>
Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com 2016-03-17 09:21:14 +01:00			`PORTNAME= trimmomatic`
biology/trimmomatic: Upgrade to 0.39 Add convenience script to run without knowing the location of the Java jar 2019-09-14 16:45:49 +02:00			`DISTVERSION= 0.39`
Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com 2016-03-17 09:21:14 +01:00			`CATEGORIES= biology java`
			`MASTER_SITES= http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/`
			`DISTNAME= Trimmomatic-${PORTVERSION}`

Multiple ports: Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org Remove Created by comments for same user Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14128 2018-01-31 02:07:07 +01:00			`MAINTAINER= jwb@FreeBSD.org`
Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com 2016-03-17 09:21:14 +01:00			`COMMENT= Flexible read trimming tool for Illumina NGS data`
Add WWW entries to port Makefiles It has been common practice to have one or more URLs at the end of the ports' pkg-descr files, one per line and prefixed with "WWW:". These URLs should point at a project website or other relevant resources. Access to these URLs required processing of the pkg-descr files, and they have often become stale over time. If more than one such URL was present in a pkg-descr file, only the first one was tarnsfered into the port INDEX, but for many ports only the last line did contain the port specific URL to further information. There have been several proposals to make a project URL available as a macro in the ports' Makefiles, over time. This commit implements such a proposal and moves one of the WWW: entries of each pkg-descr file into the respective port's Makefile. A heuristic attempts to identify the most relevant URL in case there is more than one WWW: entry in some pkg-descr file. URLs that are not moved into the Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr files in order to preserve them. There are 1256 ports that had no WWW: entries in pkg-descr files. These ports will not be touched in this commit. The portlint port has been adjusted to expect a WWW entry in each port Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as deprecated. Approved by: portmgr (tcberner) 2022-09-07 23:06:12 +02:00			`WWW= http://www.usadellab.org/cms/?page=trimmomatic`
Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com 2016-03-17 09:21:14 +01:00
			`LICENSE= GPLv3`
biology/trimmomatic: Upgrade to 0.39 Add convenience script to run without knowing the location of the Java jar 2019-09-14 16:45:49 +02:00			`LICENSE_FILE= ${WRKSRC}/LICENSE`
Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com 2016-03-17 09:21:14 +01:00
			`USES= zip`
			`USE_JAVA= yes`
biology/trimmomatic: Upgrade to 0.39 Add convenience script to run without knowing the location of the Java jar 2019-09-14 16:45:49 +02:00
Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com 2016-03-17 09:21:14 +01:00			`JAVA_RUN= yes`
			`NO_BUILD= yes`
			`NO_ARCH= yes`

biology/trimmomatic: Upgrade to 0.39 Add convenience script to run without knowing the location of the Java jar 2019-09-14 16:45:49 +02:00			`SUB_FILES= trimmomatic`

Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com 2016-03-17 09:21:14 +01:00			`do-install:`
			`${INSTALL_DATA} ${WRKSRC}/trimmomatic-${PORTVERSION}.jar \`
			`${STAGEDIR}${JAVAJARDIR}/trimmomatic.jar`
			`cd ${WRKSRC} && ${COPYTREE_SHARE} adapters ${STAGEDIR}${DATADIR}`
biology/trimmomatic: Upgrade to 0.39 Add convenience script to run without knowing the location of the Java jar 2019-09-14 16:45:49 +02:00			`${INSTALL_SCRIPT} ${WRKDIR}/trimmomatic ${STAGEDIR}${PREFIX}/bin`
Trimmomatic performs a variety of useful trimming tasks for illumina NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com 2016-03-17 09:21:14 +01:00
			`.include <bsd.port.mk>`