PORTNAME= bio-mocha
DISTVERSION= 1.20
PORTREVISION= 1
CATEGORIES= biology
MASTER_SITES= https://software.broadinstitute.org/software/mocha/
# Get this right, or ports will download bcftools in it's place via tuple
DISTFILES+= ${PORTNAME}_${DISTVERSION}-20240505.tar.gz
MAINTAINER= [email protected]
COMMENT= Bcftools plugin for mosaic chromosomal alteration analysis
WWW= https://software.broadinstitute.org/software/mocha/
LICENSE= MIT
BUILD_DEPENDS= bash:shells/bash htslib>=1.22:biology/htslib
LIB_DEPENDS= libhts.so:biology/htslib
RUN_DEPENDS= bcftools>=${PORTVERSION}:biology/bcftools
USES= autoreconf gmake localbase perl5 python:env shebangfix
USE_GITHUB= yes
USE_PERL5= test
GH_ACCOUNT= samtools
GH_PROJECT= bcftools
GH_TAGNAME= 1.22
GNU_CONFIGURE= yes
SHEBANG_FILES= misc/* test/test.pl
post-extract:
@${MV} ${WRKDIR}/*.c ${WRKDIR}/*.h ${WRKSRC}/plugins
@${MKDIR} ${WRKSRC}/MoCha
@${MV} ${WRKDIR}/*.R ${WRKSRC}/MoCha
pre-configure:
@${REINPLACE_CMD} -e 's|@PORTVERSION@|${PORTVERSION}|g' \
${WRKSRC}/configure.ac
# One .so for each .c in the mocha distfile
do-install:
${MKDIR} ${STAGEDIR}${PREFIX}/libexec/bcftools
${INSTALL_PROGRAM} ${WRKSRC}/plugins/extendFMT.so \
${STAGEDIR}${PREFIX}/libexec/bcftools
${INSTALL_PROGRAM} ${WRKSRC}/plugins/mocha.so \
${STAGEDIR}${PREFIX}/libexec/bcftools
${INSTALL_PROGRAM} ${WRKSRC}/plugins/mochatools.so \
${STAGEDIR}${PREFIX}/libexec/bcftools
(cd ${WRKSRC}/MoCha && ${COPYTREE_SHARE} . ${STAGEDIR}${DATADIR})
.include <bsd.port.mk>
