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# $NetBSD: Makefile,v 1.8 2022/04/25 14:36:19 tnn Exp $
DISTNAME= stacks-2.60
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"
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