Date: Wed, 11 Jul 2018 15:15:04 +0000 (UTC) From: Steve Wills <swills@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r474455 - in head/biology/hmmer: . files Message-ID: <201807111515.w6BFF4ON067301@repo.freebsd.org>
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Author: swills Date: Wed Jul 11 15:15:03 2018 New Revision: 474455 URL: https://svnweb.freebsd.org/changeset/ports/474455 Log: biology/hmmer: update to 3.2.1 PR: 229693 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp> (maintainer) Deleted: head/biology/hmmer/files/ Modified: head/biology/hmmer/Makefile (contents, props changed) head/biology/hmmer/distinfo (contents, props changed) head/biology/hmmer/pkg-plist (contents, props changed) Modified: head/biology/hmmer/Makefile ============================================================================== --- head/biology/hmmer/Makefile Wed Jul 11 14:46:38 2018 (r474454) +++ head/biology/hmmer/Makefile Wed Jul 11 15:15:03 2018 (r474455) @@ -2,30 +2,37 @@ # $FreeBSD$ PORTNAME= hmmer -PORTVERSION= 3.1b2 +PORTVERSION= 3.2.1 CATEGORIES= biology -MASTER_SITES= http://eddylab.org/software/hmmer3/${PORTVERSION}/ +MASTER_SITES= http://eddylab.org/software/hmmer/ MAINTAINER= mzaki@niid.go.jp COMMENT= Profile hidden Markov models for biological sequence analysis -LICENSE= GPLv3 +LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE -USES= gmake +ONLY_FOR_ARCHS= amd64 i386 ia64 powerpc powerpc64 +ONLY_FOR_ARCHS_REASON= requires SSE2 or AltiVec instructions + +USES= gmake perl5 shebangfix + GNU_CONFIGURE= yes MAKE_ARGS= V=1 +TEST_TARGET= check +USE_PERL5= test +SHEBANG_GLOB= *.pl +SHEBANG_FILES= easel/devkit/* + OPTIONS_DEFINE= DOCS EXAMPLES TEST -TEST_TEST_TARGET= check -TEST_USES= shebangfix perl5 -TEST_VARS= shebang_glob=*.pl shebang_files=easel/devkit/* use_perl5=build -DOCFILES= COPYRIGHT Userguide.pdf -EXAMPLES= 7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.out MADE1.sto \ - Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.out fn3.sto \ - globins4.hmm globins4.out globins4.sto globins45.fa \ - minifam minifam.h3f minifam.h3i minifam.h3m minifam.h3p +DOCFILES= Userguide.pdf +EXAMPLES= 7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.sto \ + Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.sto \ + globins4.hmm globins4.sto globins45.fa + +TEST_VARS= use_perl5=build post-build-TEST-on: do-test Modified: head/biology/hmmer/distinfo ============================================================================== --- head/biology/hmmer/distinfo Wed Jul 11 14:46:38 2018 (r474454) +++ head/biology/hmmer/distinfo Wed Jul 11 15:15:03 2018 (r474455) @@ -1,3 +1,3 @@ -TIMESTAMP = 1510218548 -SHA256 (hmmer-3.1b2.tar.gz) = dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536 -SIZE (hmmer-3.1b2.tar.gz) = 5965253 +TIMESTAMP = 1531293655 +SHA256 (hmmer-3.2.1.tar.gz) = a56129f9d786ec25265774519fc4e736bbc16e4076946dcbd7f2c16efc8e2b9c +SIZE (hmmer-3.2.1.tar.gz) = 7670274 Modified: head/biology/hmmer/pkg-plist ============================================================================== --- head/biology/hmmer/pkg-plist Wed Jul 11 14:46:38 2018 (r474454) +++ head/biology/hmmer/pkg-plist Wed Jul 11 15:15:03 2018 (r474455) @@ -1,10 +1,8 @@ bin/alimask bin/hmmalign bin/hmmbuild -bin/hmmc2 bin/hmmconvert bin/hmmemit -bin/hmmerfm-exactmatch bin/hmmfetch bin/hmmlogo bin/hmmpgmd @@ -18,15 +16,6 @@ bin/makehmmerdb bin/nhmmer bin/nhmmscan bin/phmmer -include/cachedb.h -include/hmmer.h -include/impl_sse.h -include/p7_config.h -include/p7_gbands.h -include/p7_gmxb.h -include/p7_gmxchk.h -include/p7_hmmcache.h -lib/libhmmer.a man/man1/alimask.1.gz man/man1/hmmalign.1.gz man/man1/hmmbuild.1.gz @@ -46,25 +35,16 @@ man/man1/makehmmerdb.1.gz man/man1/nhmmer.1.gz man/man1/nhmmscan.1.gz man/man1/phmmer.1.gz -%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT %%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/7LESS_DROME %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.hmm -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.out %%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.sto %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.hmm %%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.sto %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dna_target.fa %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.out %%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.sto %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.out %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.sto %%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3f -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3i -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3m -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3p
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