57 lines
1.8 KiB
Makefile
57 lines
1.8 KiB
Makefile
# $NetBSD$
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PKGNAME= ARC-1.1.4
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DISTNAME= ibest-ARC-v1.1.4-beta-0-g3831cb8
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CATEGORIES= biology
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MASTER_SITES= ${MASTER_SITE_GITHUB:=ibest/ARC/tarball/master/}
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MAINTAINER= pkgsrc-users@NetBSD.org
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HOMEPAGE= https://ibest.github.io/ARC/
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COMMENT= Genomics pipeline for de novo assemblies
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LICENSE= apache-2.0
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WRKSRC= ${WRKDIR}/ibest-ARC-3831cb8
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USE_TOOLS+= pax
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USE_LANGUAGES= # none
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PYDISTUTILSPKG= yes
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REPLACE_PYTHON+= ARC/exceptions.py
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REPLACE_PYTHON+= ARC/runners/assembly_checker.py
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REPLACE_PYTHON+= ARC/runners/__init__.py
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REPLACE_PYTHON+= ARC/runners/base.py
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REPLACE_PYTHON+= ARC/runners/mapper.py
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REPLACE_PYTHON+= ARC/runners/finisher.py
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REPLACE_PYTHON+= ARC/runners/assembler.py
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REPLACE_PYTHON+= ARC/__init__.py
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REPLACE_PYTHON+= ARC/logger.py
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REPLACE_PYTHON+= ARC/queue.py
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REPLACE_PYTHON+= ARC/app.py
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REPLACE_PYTHON+= ARC/process_runner.py
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REPLACE_PYTHON+= ARC/spawn.py
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REPLACE_PYTHON+= ARC/config.py
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REPLACE_PYTHON+= ARC/functions.py
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REPLACE_PYTHON+= bin/ARC
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REPLACE_PYTHON+= test_data/unit_tests.py
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DEPENDS+= blat>=3.5:../../biology/blat
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DEPENDS+= SPAdes>=3.8.2:../../biology/SPAdes
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DEPENDS+= bowtie2>=2.2.9:../../biology/bowtie2
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DEPENDS+= ${PYPKGPREFIX}-biopython>=1.63b:../../biology/py-biopython
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DEPENDS+= ${PYPKGPREFIX}-sqlite3>=${PY_DISTVERSION}:../../databases/py-sqlite3
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INSTALLATION_DIRS+= share/doc/ARC share/examples/ARC
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NONEXECUTABLE_FILES+= test_data/clean test_data/runarc
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post-extract:
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.for f in ${NONEXECUTABLE_FILES}
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${CHMOD} a-x ${WRKSRC}/${f}
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.endfor
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post-install:
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${INSTALL_DATA} ${WRKSRC}/docs/Pipeline.pdf ${DESTDIR}${PREFIX}/share/doc/ARC
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cd ${WRKSRC}/test_data && ${PAX} -rw . ${DESTDIR}${PREFIX}/share/examples/ARC
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${RM} -f ${DESTDIR}${PREFIX}/share/examples/ARC/runarc.orig
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.include "../../lang/python/application.mk"
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.include "../../lang/python/extension.mk"
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.include "../../mk/bsd.pkg.mk"
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