svn commit: r453972 - in head/biology/hmmer: . files
Wen Heping
wen at FreeBSD.org
Sat Nov 11 12:51:54 UTC 2017
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 at niid.go.jp
Approved by: bacon4000 at 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 at gmail.com
+MAINTAINER= mzaki at 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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