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)
This commit is contained in:
Yuri Victorovich 2018-03-10 06:21:37 +00:00
parent 6d4a8a5d1f
commit 1af9914df9
Notes: 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 @@
# $FreeBSD$
PORTNAME= seqan-apps
PORTVERSION= 2.2.0
DISTVERSIONPREFIX= seqan-v
PORTREVISION= 9
DISTVERSION= 2.4.0
CATEGORIES= biology
MAINTAINER= h2+fbsdports@fsfe.org
COMMENT= Official Bioinformatic applications based on the SeqAn library
COMMENT= Official bioinformatic applications based on the SeqAn library
LICENSE= BSD3CLAUSE LGPL3 GPLv3
LICENSE_COMB= multi
BUILD_DEPENDS= boost-libs>0:devel/boost-libs
BROKEN_aarch64= fails to compile: Error: unknown mnemonic rep -- rep
BROKEN_armv6= fails to compile: Error: bad instruction rep
BROKEN_armv7= fails to compile: Error: bad instruction rep
BROKEN_powerpc64= fails to compile: Error: unrecognized opcode: rep
USES= cmake:outsource compiler:openmp # once #199603 is resolved, add c++14-lang
USE_GITHUB= yes
GH_ACCOUNT= seqan
GH_PROJECT= seqan
# once #199603 is resolved, do the following instead of USE_GCC
# USES= cmake:outsource compiler:openmp,c++14-lang
USES= cmake:outsource
CMAKE_ARGS= -DSEQAN_BUILD_SYSTEM="SEQAN_RELEASE_APPS"
USE_GCC= yes
OPTIONS_RADIO= ARCH
OPTIONS_RADIO_ARCH= SSE4 AVX2 NATIVE
SSE4_DESC= Use SSE4 and POPCNT instructions
SSE4_CMAKE_ON= -DSEQAN_ARCH_SSE4:BOOL=TRUE
AVX2_DESC= Use SSE4, AVX2 and POPCNT instructions
AVX2_CMAKE_ON= -DSEQAN_ARCH_AVX2:BOOL=TRUE
NATIVE_DESC= Use all available instruction sets (-march=native)
NATIVE_CMAKE_ON= -DSEQAN_ARCH_NATIVE:BOOL=TRUE
.include <bsd.port.pre.mk>

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@ -1,3 +1,3 @@
TIMESTAMP = 1473848209
SHA256 (seqan-seqan-seqan-v2.2.0_GH0.tar.gz) = 6add074932c2723ef1fb658c88f906bdd6ced1fc34cb16a7410251ffc4cb8cc8
SIZE (seqan-seqan-seqan-v2.2.0_GH0.tar.gz) = 110936119
TIMESTAMP = 1517833288
SHA256 (seqan-seqan-seqan-v2.4.0_GH0.tar.gz) = d7084d17729214003e84818e0280a16f223c8f1c6a30eeef040c27e0c0047bd7
SIZE (seqan-seqan-seqan-v2.4.0_GH0.tar.gz) = 109626901

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@ -48,6 +48,7 @@ bin/stellar
bin/tree_recon
bin/yara_indexer
bin/yara_mapper
man/man1/sak.1.gz
share/doc/alf/LICENSE
share/doc/alf/README
share/doc/alf/example/small.fasta
@ -117,7 +118,6 @@ share/doc/rep_sep/README
share/doc/sak/LICENSE
share/doc/sak/README
share/doc/sak/README.sak.txt
share/doc/sak/man/sak.1
share/doc/sam2matrix/LICENSE
share/doc/sam2matrix/README
share/doc/samcat/LICENSE

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@ -2,30 +2,35 @@
# $FreeBSD$
PORTNAME= seqan
PORTVERSION= 2.2.0
DISTVERSION= 2.4.0
CATEGORIES= biology
MASTER_SITES= http://packages.seqan.de/seqan-library/
DISTNAME= ${PORTNAME}-library-${PORTVERSION}
MAINTAINER= h2+fbsdports@fsfe.org
COMMENT= C++ Sequence Analysis Template Library
COMMENT= C++ sequence analysis template library
LICENSE= BSD3CLAUSE
LICENSE_FILE= ${WRKSRC}/share/doc/seqan/LICENSE
USES= tar:xz
NO_BUILD= yes
NO_ARCH= yes
CONFLICTS= seqan1-[0-9]*
OPTIONS_DEFINE= DOCS
DOCS_DESC= Install official API documentation (html)
PORTDOCS= *
post-patch: # delete empty doc dirs
@cd ${WRKSRC}/share/doc/seqan/html && ${RMDIR} docs/seqan docs lists
do-install:
cd ${WRKSRC}/include/ && ${COPYTREE_SHARE} ./${PORTNAME} ${STAGEDIR}/${PREFIX}/include
${MKDIR} ${STAGEDIR}/${PREFIX}/share/cmake/Modules
${INSTALL_DATA} ${WRKSRC}/share/cmake/Modules/FindSeqAn.cmake ${STAGEDIR}/${PREFIX}/share/cmake/Modules/
${MKDIR} ${STAGEDIR}/${PREFIX}/libdata/pkgconfig
@${MKDIR} ${STAGEDIR}/${PREFIX}/lib/cmake/seqan
${INSTALL_DATA} ${WRKSRC}/share/cmake/seqan/seqan-config.cmake ${STAGEDIR}/${PREFIX}/lib/cmake/seqan/
@${MKDIR} ${STAGEDIR}/${PREFIX}/libdata/pkgconfig
${INSTALL_DATA} ${WRKSRC}/share/pkgconfig/seqan-2.pc ${STAGEDIR}/${PREFIX}/libdata/pkgconfig/
do-install-DOCS-on:

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@ -1,3 +1,3 @@
TIMESTAMP = 1473846790
SHA256 (seqan-library-2.2.0.tar.xz) = b5c036a3d2fc2fe5f2d57dcd4d7c523a6df146ab7b44bc789f42004b058d72fd
SIZE (seqan-library-2.2.0.tar.xz) = 5223004
TIMESTAMP = 1517832492
SHA256 (seqan-library-2.4.0.tar.xz) = dd97b1514ab83acb7d7be911b157979e188e8ca72cc61c430c1e0fd03bcd41a5
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
focus on biological data. The library is licensed under the
3-clause BSD license except the applications which are GPL.
This port now only contains the header library and API
documentation. The apps are separate.
This port only contains the header library and API documentation.
The apps are installed by biology/seqan-apps.
WWW: http://www.seqan.de/
WWW: https://www.seqan.de/

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