mirror of
https://git.FreeBSD.org/ports.git
synced 2024-12-23 04:23:08 +00:00
ea8c8ec7da
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, everything INDEX-11 shows with a dependency on lang/gcc9 now. PR: 238330
69 lines
1.8 KiB
Makefile
69 lines
1.8 KiB
Makefile
# $FreeBSD$
|
|
|
|
PORTNAME= dDocent
|
|
DISTVERSIONPREFIX= v
|
|
DISTVERSION= 2.7.8
|
|
PORTREVISION= 1
|
|
CATEGORIES= biology java perl5 python
|
|
|
|
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 \
|
|
fastp:biology/fastp
|
|
|
|
USES= perl5 python shebangfix
|
|
USE_JAVA= yes
|
|
USE_GITHUB= yes
|
|
|
|
SHEBANG_FILES= dDocent scripts/*.sh scripts/*.pl scripts/dDocent_filters
|
|
GH_ACCOUNT= jpuritz
|
|
|
|
NO_BUILD= yes
|
|
NO_ARCH= yes
|
|
|
|
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
|
|
|
|
# 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:
|
|
@${REINPLACE_CMD} -i '' \
|
|
-e 's|SHELL=bash|SHELL=${LOCALBASE}/bin/bash|g' \
|
|
-e 's|python|${PYTHON_CMD}|g' \
|
|
${STAGEDIR}${PREFIX}/bin/dDocent
|
|
|
|
.include <bsd.port.mk>
|