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pkgsrc/biology/plinkseq/Makefile

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revbump for devel/protobuf
2022-04-03 20:50:16 +02:00
# $NetBSD: Makefile,v 1.11 2022/04/03 18:50:17 adam Exp $
Import PLINK/SEQ version 0.08 as biology/plinkseq Packaged by Jason Bacon for pkgsrc-wip. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
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DISTNAME= plinkseq-0.08
revbump for devel/protobuf
2022-04-03 20:50:16 +02:00
PKGREVISION= 6
Import PLINK/SEQ version 0.08 as biology/plinkseq Packaged by Jason Bacon for pkgsrc-wip. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
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CATEGORIES= biology
plinkseq: use https
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MASTER_SITES= https://atgu.mgh.harvard.edu/plinkseq/dist/version-0.08/
Import PLINK/SEQ version 0.08 as biology/plinkseq Packaged by Jason Bacon for pkgsrc-wip. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
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Multiple packages: Replace obsolete maintainer email jwbacon@tds.net ==> bacon@NetBSD.org
2019-01-13 23:06:42 +01:00
MAINTAINER= bacon@NetBSD.org
plinkseq: use https
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HOMEPAGE= https://atgu.mgh.harvard.edu/plinkseq/
Import PLINK/SEQ version 0.08 as biology/plinkseq Packaged by Jason Bacon for pkgsrc-wip. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
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COMMENT= C/C++ library for working with human genetic variation data
LICENSE= gnu-gpl-v2 # Assuming same as plink. No info on web.
GNU_CONFIGURE= yes
USE_LIBTOOL= yes
biology/plinkseq: Requires c++11 to build with protobuf-3.6.0
2018-08-04 23:42:28 +02:00
USE_LANGUAGES= c c++11
Import PLINK/SEQ version 0.08 as biology/plinkseq Packaged by Jason Bacon for pkgsrc-wip. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
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USE_TOOLS= bash:run
REPLACE_BASH= browser/pbrowse.in index/index.in
fix build on SunOS
2014-02-08 13:27:14 +01:00
LDFLAGS.SunOS+= -lsocket -lnsl
Import PLINK/SEQ version 0.08 as biology/plinkseq Packaged by Jason Bacon for pkgsrc-wip. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
2012-11-01 05:06:21 +01:00
.include "../../mk/bsd.prefs.mk"
Fixed pkglint warnings.
2016-12-17 13:55:29 +01:00
.if ${OPSYS} != "Linux"
Import PLINK/SEQ version 0.08 as biology/plinkseq Packaged by Jason Bacon for pkgsrc-wip. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
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BUILDLINK_TRANSFORM= rm:-ldl
.endif
Fix build against newer protocol buffers library. Regenerate source from missing protocol description fetched from: https://bitbucket.org/statgen/plinkseq/raw/976c492c6e11e81aa798e2c4c20bcf17ea4073a1/lib/variant.proto https://bitbucket.org/statgen/plinkseq/raw/976c492c6e11e81aa798e2c4c20bcf17ea4073a1/lib/pp.proto Bump PKGREVISION.
2013-03-26 21:11:19 +01:00
# Put missing protocol description files in place:
post-extract:
Fixed pkglint warnings.
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${CP} ${FILESDIR}/pp.proto ${WRKSRC}/lib/
${CP} ${FILESDIR}/variant.proto ${WRKSRC}/lib/
Fix build against newer protocol buffers library. Regenerate source from missing protocol description fetched from: https://bitbucket.org/statgen/plinkseq/raw/976c492c6e11e81aa798e2c4c20bcf17ea4073a1/lib/variant.proto https://bitbucket.org/statgen/plinkseq/raw/976c492c6e11e81aa798e2c4c20bcf17ea4073a1/lib/pp.proto Bump PKGREVISION.
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# Regenerate:
pre-build:
Fixed pkglint warnings.
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cd ${WRKSRC}/lib && protoc --cpp_out=. pp.proto && mv pp.pb.cc pp.pb.cpp
cd ${WRKSRC}/lib && protoc --cpp_out=. variant.proto && mv variant.pb.cc variant.pb.cpp
Fix build against newer protocol buffers library. Regenerate source from missing protocol description fetched from: https://bitbucket.org/statgen/plinkseq/raw/976c492c6e11e81aa798e2c4c20bcf17ea4073a1/lib/variant.proto https://bitbucket.org/statgen/plinkseq/raw/976c492c6e11e81aa798e2c4c20bcf17ea4073a1/lib/pp.proto Bump PKGREVISION.
2013-03-26 21:11:19 +01:00
Import PLINK/SEQ version 0.08 as biology/plinkseq Packaged by Jason Bacon for pkgsrc-wip. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
2012-11-01 05:06:21 +01:00
.include "../../devel/protobuf/buildlink3.mk"
.include "../../mk/bsd.pkg.mk"
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