Date: Sat, 11 Nov 2017 12:51:52 +0000 (UTC) From: Wen Heping <wen@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r453972 - in head/biology/hmmer: . files Message-ID: <201711111251.vABCpqWd007222@repo.freebsd.org>
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Author: wen Date: Sat Nov 11 12:51:52 2017 New Revision: 453972 URL: https://svnweb.freebsd.org/changeset/ports/453972 Log: - Update to 3.1b2 - Pass maintainership to submitter PR: 223561 Submitted by: mzaki@niid.go.jp Approved by: bacon4000@gmail.com(previous maintainer) Added: head/biology/hmmer/files/ head/biology/hmmer/files/patch-configure (contents, props changed) Modified: head/biology/hmmer/Makefile head/biology/hmmer/distinfo head/biology/hmmer/pkg-descr head/biology/hmmer/pkg-plist Modified: head/biology/hmmer/Makefile ============================================================================== --- head/biology/hmmer/Makefile Sat Nov 11 12:48:53 2017 (r453971) +++ head/biology/hmmer/Makefile Sat Nov 11 12:51:52 2017 (r453972) @@ -2,47 +2,41 @@ # $FreeBSD$ PORTNAME= hmmer -PORTVERSION= 3.0 -PORTREVISION= 1 +PORTVERSION= 3.1b2 CATEGORIES= biology -MASTER_SITES= ftp://selab.janelia.org/pub/software/hmmer3/3.0/ \ - http://selab.janelia.org/software/hmmer3/3.0/ +MASTER_SITES= http://eddylab.org/software/hmmer3/${PORTVERSION}/ -MAINTAINER= bacon4000@gmail.com +MAINTAINER= mzaki@niid.go.jp COMMENT= Profile hidden Markov models for biological sequence analysis -BROKEN= No public distfiles - LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE +USES= gmake GNU_CONFIGURE= yes -USES= perl5 -CONFIGURE_ARGS+=--enable-threads +MAKE_ARGS= V=1 -DOCFILES= COPYRIGHT INSTALL LICENSE Userguide.pdf -EXAMPLES= 7LESS_DROME Pkinase.sto fn3.sto globins4.sto minifam.h3f minifam.h3p \ - HBB_HUMAN fn3.hmm globins4.hmm globins45.fa minifam.h3i \ - Pkinase.hmm fn3.out globins4.out minifam minifam.h3m +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 -OPTIONS_DEFINE= DOCS EXAMPLES +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 -.include <bsd.port.options.mk> +post-build-TEST-on: do-test -# HMMER is useless without SSE and any PC in use today should support it -# Should probably also do enable-vmx on Power processors to enable -# Altivec/VMX, but I don't have a machine to test this. -.if ${ARCH} == "amd64" || ${ARCH} == "i386" -CONFIGURE_ARGS+=--enable-sse -.endif - post-install: @${STRIP_CMD} ${STAGEDIR}${PREFIX}/bin/* - (cd ${WRKSRC}/documentation/man; for i in *.man; do \ - ${INSTALL_MAN} $$i ${STAGEDIR}${PREFIX}/man/man1/`echo $$i|${SED} 's/.man/.1/'`; \ - done) + +post-install-DOCS-on: @${MKDIR} ${STAGEDIR}${DOCSDIR} ${INSTALL_DATA} ${DOCFILES:S,^,${WRKSRC}/,} ${STAGEDIR}${DOCSDIR} + +post-install-EXAMPLES-on: @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} ${INSTALL_DATA} ${EXAMPLES:S,^,${WRKSRC}/tutorial/,} ${STAGEDIR}${EXAMPLESDIR} Modified: head/biology/hmmer/distinfo ============================================================================== --- head/biology/hmmer/distinfo Sat Nov 11 12:48:53 2017 (r453971) +++ head/biology/hmmer/distinfo Sat Nov 11 12:51:52 2017 (r453972) @@ -1,2 +1,3 @@ -SHA256 (hmmer-3.0.tar.gz) = 6977e6473fcb554b1d5a86dc9edffffa53918c1bd88d7fd20d7499f1ba719e83 -SIZE (hmmer-3.0.tar.gz) = 3952015 +TIMESTAMP = 1510218548 +SHA256 (hmmer-3.1b2.tar.gz) = dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536 +SIZE (hmmer-3.1b2.tar.gz) = 5965253 Added: head/biology/hmmer/files/patch-configure ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hmmer/files/patch-configure Sat Nov 11 12:51:52 2017 (r453972) @@ -0,0 +1,10 @@ +--- configure.orig 2015-02-26 12:45:55 UTC ++++ configure +@@ -3912,6 +3912,7 @@ fi + if test "$impl_choice" = "none"; then + case $host in + ia64-*-*) impl_choice=sse;; ++ amd64-*-*) impl_choice=sse;; + i?86-*-*) impl_choice=sse;; + x86*-*-*) impl_choice=sse;; + powerpc*-*-*) impl_choice=vmx;; Modified: head/biology/hmmer/pkg-descr ============================================================================== --- head/biology/hmmer/pkg-descr Sat Nov 11 12:48:53 2017 (r453971) +++ head/biology/hmmer/pkg-descr Sat Nov 11 12:51:52 2017 (r453972) @@ -7,4 +7,4 @@ model called a "hidden Markov model" which can then be a sequence database to find (and/or align) additional homologues of the sequence family. -WWW: http://hmmer.janelia.org/ +WWW: http://hmmer.org/ Modified: head/biology/hmmer/pkg-plist ============================================================================== --- head/biology/hmmer/pkg-plist Sat Nov 11 12:48:53 2017 (r453971) +++ head/biology/hmmer/pkg-plist Sat Nov 11 12:51:52 2017 (r453972) @@ -1,45 +1,70 @@ +bin/alimask bin/hmmalign bin/hmmbuild +bin/hmmc2 bin/hmmconvert bin/hmmemit +bin/hmmerfm-exactmatch bin/hmmfetch +bin/hmmlogo +bin/hmmpgmd bin/hmmpress bin/hmmscan bin/hmmsearch bin/hmmsim bin/hmmstat bin/jackhmmer +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 man/man1/hmmconvert.1.gz man/man1/hmmemit.1.gz man/man1/hmmer.1.gz man/man1/hmmfetch.1.gz +man/man1/hmmlogo.1.gz +man/man1/hmmpgmd.1.gz man/man1/hmmpress.1.gz man/man1/hmmscan.1.gz man/man1/hmmsearch.1.gz man/man1/hmmsim.1.gz man/man1/hmmstat.1.gz man/man1/jackhmmer.1.gz +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%%/INSTALL -%%PORTDOCS%%%%DOCSDIR%%/LICENSE %%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/7LESS_DROME -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.sto -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.sto -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.sto -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3f -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3p %%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3i +%%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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