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# $FreeBSD$
PORTNAME= dDocent
DISTVERSIONPREFIX= v
DISTVERSION= 2.2.25
PORTREVISION= 1
CATEGORIES= biology java
MAINTAINER= jwb@FreeBSD.org
COMMENT= Bash pipeline for RAD sequencing
LICENSE= MIT
# ddocent test data do not unpack with FreeBSD 11.1 /usr/bin/unzip
RUN_DEPENDS= unzip>=0:archivers/unzip \
mawk>=0:lang/mawk \
gawk>=0:lang/gawk \
coreutils>=0:sysutils/coreutils \
gnuplot>=0:math/gnuplot \
parallel>=0:sysutils/parallel \
bash:shells/bash \
bwa>=0.7.13:biology/bwa \
cd-hit>=0:biology/cd-hit \
samtools>=1.3:biology/samtools \
vcftools>=0.1.15:biology/vcftools \
trimmomatic>=0:biology/trimmomatic \
bamtools>=0:biology/bamtools \
stacks>=0:biology/stacks \
rainbow>=0:biology/rainbow \
trimadap>=0:biology/trimadap \
seqtk>=0:biology/seqtk \
bedtools>=2.26.0:biology/bedtools \
pear-merger>=0:biology/pear-merger \
vcflib>=0:biology/vcflib \
freebayes:biology/freebayes
USES= perl5 python shebangfix
SHEBANG_FILES= dDocent scripts/*.sh scripts/*.pl scripts/dDocent_filters
USE_JAVA= yes
USE_GITHUB= yes
GH_ACCOUNT= jpuritz
NO_BUILD= yes
NO_ARCH= yes
# These are on top of patch-dDocent, so don't apply them within the source
# tree, or they'll get picked up by patch generators, and hard-code PREFIX.
post-install:
${REINPLACE_CMD} -i '' \
-e 's|%%PREFIX%%|${PREFIX}|g' \
-e 's|%%JAVAJARDIR%%|${JAVAJARDIR}|g' \
-e 's|%%BASH%%|${LOCALBASE}/bin/bash|g' \
-e 's|python|${PYTHON_CMD}|g' \
${STAGEDIR}${PREFIX}/bin/dDocent
do-install:
${MKDIR} ${STAGEDIR}${PREFIX}/bin
${INSTALL_SCRIPT} \
${WRKSRC}/dDocent \
${WRKSRC}/*.sh \
${FILESDIR}/ddocent-assembly-test \
${FILESDIR}/ddocent-assembly-test-cleanup \
${WRKSRC}/scripts/*.sh \
${WRKSRC}/scripts/*.pl \
${WRKSRC}/scripts/dDocent_filters \
${STAGEDIR}${PREFIX}/bin
.include <bsd.port.mk>
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