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| author | Yuri Victorovich <yuri@FreeBSD.org> | 2018-03-10 06:21:37 +0000 |
|---|---|---|
| committer | Yuri Victorovich <yuri@FreeBSD.org> | 2018-03-10 06:21:37 +0000 |
| commit | 1af9914df9277a1b8678da8c4a4ee51ff6841a82 (patch) | |
| tree | fea76f19685ea567c95e91bf74ab4536e153b256 /biology/seqan-apps | |
| parent | 6d4a8a5d1f408569244f4fbf9b47a3b7c1791650 (diff) | |
| download | ports-1af9914df9277a1b8678da8c4a4ee51ff6841a82.tar.gz ports-1af9914df9277a1b8678da8c4a4ee51ff6841a82.zip | |
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)
Notes
Notes:
svn path=/head/; revision=464043
Diffstat (limited to 'biology/seqan-apps')
| -rw-r--r-- | biology/seqan-apps/Makefile | 24 | ||||
| -rw-r--r-- | biology/seqan-apps/distinfo | 6 | ||||
| -rw-r--r-- | biology/seqan-apps/pkg-plist | 2 |
3 files changed, 15 insertions, 17 deletions
diff --git a/biology/seqan-apps/Makefile b/biology/seqan-apps/Makefile index 10c6ee5a0174..9349cd136323 100644 --- a/biology/seqan-apps/Makefile +++ b/biology/seqan-apps/Makefile @@ -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> diff --git a/biology/seqan-apps/distinfo b/biology/seqan-apps/distinfo index 998a68b9493c..7da9e67cfac1 100644 --- a/biology/seqan-apps/distinfo +++ b/biology/seqan-apps/distinfo @@ -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 diff --git a/biology/seqan-apps/pkg-plist b/biology/seqan-apps/pkg-plist index 747936672f94..8b8e5ba425e3 100644 --- a/biology/seqan-apps/pkg-plist +++ b/biology/seqan-apps/pkg-plist @@ -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 |