48 lines
1.3 KiB
Makefile
48 lines
1.3 KiB
Makefile
# $NetBSD: Makefile,v 1.10 2022/06/30 11:18:05 nia Exp $
|
|
|
|
DISTNAME= stacks-2.60
|
|
PKGREVISION= 2
|
|
CATEGORIES= biology
|
|
MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/
|
|
|
|
MAINTAINER= bacon@NetBSD.org
|
|
HOMEPAGE= http://catchenlab.life.illinois.edu/stacks/
|
|
COMMENT= Software pipeline for building loci from short-read sequences
|
|
LICENSE= gnu-gpl-v2
|
|
|
|
USE_LANGUAGES= c c++14
|
|
USE_TOOLS+= bash perl:run
|
|
GNU_CONFIGURE= yes
|
|
|
|
REPLACE_BASH+= scripts/stacks-count-reads-per-sample-per-locus
|
|
REPLACE_BASH+= scripts/stacks-dist-extract
|
|
REPLACE_BASH+= scripts/stacks-gdb
|
|
REPLACE_BASH+= scripts/stacks-samtools-tview
|
|
REPLACE_PERL= scripts/*.pl
|
|
REPLACE_PYTHON+= scripts/*.py
|
|
REPLACE_PYTHON+= scripts/stacks-integrate-alignments
|
|
|
|
REPLACE_INTERPRETER+= Rscript
|
|
REPLACE.Rscript.old= .*Rscript
|
|
REPLACE.Rscript.new= ${PREFIX}/bin/Rscript
|
|
REPLACE_FILES.Rscript= scripts/stacks-hist2d-loci-samples-coverage
|
|
|
|
.include "../../mk/bsd.prefs.mk"
|
|
|
|
.if ${OPSYS} == Darwin
|
|
# pkgsrc sed wrapper lacks -i
|
|
SUBST_CLASSES+= sed
|
|
SUBST_STAGE.sed= pre-configure
|
|
SUBST_FILES.sed= Makefile.in
|
|
SUBST_SED.sed= -e 's|sed -i.bkp|/usr/bin/sed -i .bkp|'
|
|
.else
|
|
# macOS clang lacks OpenMP
|
|
CFLAGS+= -fopenmp
|
|
.endif
|
|
|
|
LDFLAGS.SunOS+= -lsocket
|
|
|
|
.include "../../lang/python/application.mk"
|
|
.include "../../math/R/buildlink3.mk"
|
|
.include "../../devel/zlib/buildlink3.mk"
|
|
.include "../../mk/bsd.pkg.mk"
|