biology/seqan-apps, biology/seqan: Update to 2.4.0
Port changes for biology/seqan-apps: * Changed to DISTVERSION * Updated COMMENT * Added USES=compiler:openmp * Removed BROKEN_xx (upstream now claims support for these architectures) * Removed USE_GCC * Added SSE4/AVX2/NATIVE SIMD options Port changes for biology/seqan: * Changed to DISTVERSION * Added NO_ARCH * Added PORTDOCS=* * Updated do-install PR: 225682 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org> (maintainer) Approved by: tcberner (mentor, implicit)
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svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=464043
7 changed files with 90 additions and 1269 deletions
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@ -2,34 +2,32 @@
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# $FreeBSD$
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PORTNAME= seqan-apps
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PORTVERSION= 2.2.0
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DISTVERSIONPREFIX= seqan-v
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PORTREVISION= 9
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DISTVERSION= 2.4.0
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CATEGORIES= biology
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MAINTAINER= h2+fbsdports@fsfe.org
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COMMENT= Official Bioinformatic applications based on the SeqAn library
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COMMENT= Official bioinformatic applications based on the SeqAn library
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LICENSE= BSD3CLAUSE LGPL3 GPLv3
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LICENSE_COMB= multi
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BUILD_DEPENDS= boost-libs>0:devel/boost-libs
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BROKEN_aarch64= fails to compile: Error: unknown mnemonic rep -- rep
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BROKEN_armv6= fails to compile: Error: bad instruction rep
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BROKEN_armv7= fails to compile: Error: bad instruction rep
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BROKEN_powerpc64= fails to compile: Error: unrecognized opcode: rep
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USES= cmake:outsource compiler:openmp # once #199603 is resolved, add c++14-lang
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USE_GITHUB= yes
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GH_ACCOUNT= seqan
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GH_PROJECT= seqan
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# once #199603 is resolved, do the following instead of USE_GCC
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# USES= cmake:outsource compiler:openmp,c++14-lang
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USES= cmake:outsource
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CMAKE_ARGS= -DSEQAN_BUILD_SYSTEM="SEQAN_RELEASE_APPS"
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USE_GCC= yes
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OPTIONS_RADIO= ARCH
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OPTIONS_RADIO_ARCH= SSE4 AVX2 NATIVE
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SSE4_DESC= Use SSE4 and POPCNT instructions
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SSE4_CMAKE_ON= -DSEQAN_ARCH_SSE4:BOOL=TRUE
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AVX2_DESC= Use SSE4, AVX2 and POPCNT instructions
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AVX2_CMAKE_ON= -DSEQAN_ARCH_AVX2:BOOL=TRUE
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NATIVE_DESC= Use all available instruction sets (-march=native)
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NATIVE_CMAKE_ON= -DSEQAN_ARCH_NATIVE:BOOL=TRUE
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.include <bsd.port.pre.mk>
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@ -1,3 +1,3 @@
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TIMESTAMP = 1473848209
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SHA256 (seqan-seqan-seqan-v2.2.0_GH0.tar.gz) = 6add074932c2723ef1fb658c88f906bdd6ced1fc34cb16a7410251ffc4cb8cc8
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SIZE (seqan-seqan-seqan-v2.2.0_GH0.tar.gz) = 110936119
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TIMESTAMP = 1517833288
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SHA256 (seqan-seqan-seqan-v2.4.0_GH0.tar.gz) = d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7
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SIZE (seqan-seqan-seqan-v2.4.0_GH0.tar.gz) = 109626901
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@ -48,6 +48,7 @@ bin/stellar
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bin/tree_recon
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bin/yara_indexer
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bin/yara_mapper
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man/man1/sak.1.gz
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share/doc/alf/LICENSE
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share/doc/alf/README
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share/doc/alf/example/small.fasta
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@ -117,7 +118,6 @@ share/doc/rep_sep/README
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share/doc/sak/LICENSE
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share/doc/sak/README
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share/doc/sak/README.sak.txt
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share/doc/sak/man/sak.1
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share/doc/sam2matrix/LICENSE
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share/doc/sam2matrix/README
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share/doc/samcat/LICENSE
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@ -2,30 +2,35 @@
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# $FreeBSD$
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PORTNAME= seqan
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PORTVERSION= 2.2.0
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DISTVERSION= 2.4.0
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CATEGORIES= biology
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MASTER_SITES= http://packages.seqan.de/seqan-library/
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DISTNAME= ${PORTNAME}-library-${PORTVERSION}
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MAINTAINER= h2+fbsdports@fsfe.org
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COMMENT= C++ Sequence Analysis Template Library
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COMMENT= C++ sequence analysis template library
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LICENSE= BSD3CLAUSE
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LICENSE_FILE= ${WRKSRC}/share/doc/seqan/LICENSE
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USES= tar:xz
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NO_BUILD= yes
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NO_ARCH= yes
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CONFLICTS= seqan1-[0-9]*
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OPTIONS_DEFINE= DOCS
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DOCS_DESC= Install official API documentation (html)
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PORTDOCS= *
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post-patch: # delete empty doc dirs
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@cd ${WRKSRC}/share/doc/seqan/html && ${RMDIR} docs/seqan docs lists
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do-install:
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cd ${WRKSRC}/include/ && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include
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${MKDIR} ${STAGEDIR}/${PREFIX}/share/cmake/Modules
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${INSTALL_DATA} ${WRKSRC}/share/cmake/Modules/FindSeqAn.cmake ${STAGEDIR}/${PREFIX}/share/cmake/Modules/
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${MKDIR} ${STAGEDIR}/${PREFIX}/libdata/pkgconfig
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@${MKDIR} ${STAGEDIR}/${PREFIX}/lib/cmake/seqan
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${INSTALL_DATA} ${WRKSRC}/share/cmake/seqan/seqan-config.cmake ${STAGEDIR}/${PREFIX}/lib/cmake/seqan/
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@${MKDIR} ${STAGEDIR}/${PREFIX}/libdata/pkgconfig
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${INSTALL_DATA} ${WRKSRC}/share/pkgconfig/seqan-2.pc ${STAGEDIR}/${PREFIX}/libdata/pkgconfig/
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do-install-DOCS-on:
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@ -1,3 +1,3 @@
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TIMESTAMP = 1473846790
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SHA256 (seqan-library-2.2.0.tar.xz) = b5c036a3d2fc2fe5f2d57dcd4d7c523a6df146ab7b44bc789f42004b058d72fd
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SIZE (seqan-library-2.2.0.tar.xz) = 5223004
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TIMESTAMP = 1517832492
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SHA256 (seqan-library-2.4.0.tar.xz) = dd97b1514ab83acb7d7be911b157979e188e8ca72cc61c430c1e0fd03bcd41a5
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SIZE (seqan-library-2.4.0.tar.xz) = 4868868
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@ -3,7 +3,7 @@ and data structures for the analysis of sequences with the
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focus on biological data. The library is licensed under the
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3-clause BSD license except the applications which are GPL.
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This port now only contains the header library and API
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documentation. The apps are separate.
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This port only contains the header library and API documentation.
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The apps are installed by biology/seqan-apps.
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WWW: http://www.seqan.de/
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WWW: https://www.seqan.de/
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