PORTNAME= bbmap
DISTVERSION= 39.34
CATEGORIES= biology java
MASTER_SITES= SF/bbmap/
DISTNAME= BBMap_${PORTVERSION}
MAINTAINER= [email protected]
COMMENT= BBMap short read aligner, and other bioinformatic tools
WWW= https://jgi.doe.gov/data-and-tools/bbtools/ \
https://sourceforge.net/projects/bbmap/ \
https://bitbucket.org/berkeleylab/jgi-bbtools/src/master/
LICENSE= BSD3CLAUSE
LICENSE_FILE= ${WRKSRC}/license.txt
RUN_DEPENDS= bash:shells/bash \
pbzip2:archivers/pbzip2 \
pigz:archivers/pigz
USES= java shebangfix
SHEBANG_FILES= ${WRKSRC}/*.sh
NO_ARCH= yes
NO_BUILD= yes
WRKSRC= ${WRKDIR}/${PORTNAME}
LIBEXEC_DIR= ${PREFIX}/libexec/bbmap
pre-configure:
${REINPLACE_CMD} -e 's|"$$DIR""current/"|${JAVAJARDIR}/bbmap|g' \
${WRKSRC}/*.sh
${REINPLACE_CMD} \
-e 's|"$$DIR""/calcmem.sh"|${LIBEXEC_DIR}/bbmap/calcmem.sh|g' \
${WRKSRC}/*.sh
# FIXME: Find out which scripts are meant to be part of the CLI
do-install:
@${MKDIR} ${STAGEDIR}${LIBEXEC_DIR}
@${MKDIR} ${STAGEDIR}${JAVAJARDIR}/bbmap
${INSTALL_SCRIPT} ${WRKSRC}/*.sh ${STAGEDIR}${LIBEXEC_DIR}
cd ${WRKSRC}/current && ${COPYTREE_SHARE} . \
${STAGEDIR}${JAVAJARDIR}/bbmap
.for f in bbduk.sh bbnorm.sh dedupe.sh bbmap.sh bloomfilter.sh reformat.sh \
bbmerge.sh tadpole.sh
${RLN} ${STAGEDIR}${LIBEXEC_DIR}/${f} ${STAGEDIR}${PREFIX}/bin
.endfor
.include <bsd.port.mk>
