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
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
|
|
@ -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>
|
||||
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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:
|
||||
|
|
|
|||
|
|
@ -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
|
||||
|
|
|
|||
|
|
@ -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/
|
||||
|
|
|
|||
File diff suppressed because it is too large
Load diff
Loading…
Reference in a new issue