Attachment 187879 Details for Bug 223561 – svn diff for biology/hmmer

[patch] svn diff for biology/hmmer

hmmer.diff (text/plain), 5.46 KB, created by Motomichi Matsuzaki on 2017-11-09 11:57:24 UTC

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Creator: Motomichi Matsuzaki

Created: 2017-11-09 11:57:24 UTC

Size: 5.46 KB

patch

obsolete

>Index: Makefile
>===================================================================
>--- Makefile	(revision 453805)
>+++ Makefile	(working copy)
>@@ -2,32 +2,32 @@
> # $FreeBSD$
> 
> 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
> COMMENT=	Profile hidden Markov models for biological sequence analysis
> 
>-BROKEN=		No public distfiles
>-
> LICENSE=	GPLv3
> LICENSE_FILE=	${WRKSRC}/LICENSE
> 
>+USES=		gmake
> GNU_CONFIGURE=	yes
>-USES=		perl5
>-CONFIGURE_ARGS+=--enable-threads
>+MAKE_ARGS=	V=1
> 
>-DOCFILES=	COPYRIGHT INSTALL LICENSE Userguide.pdf
>-EXAMPLES=	7LESS_DROME Pkinase.sto fn3.sto globins4.sto minifam.h3f minifam.h3p \
>-		HBB_HUMAN fn3.hmm globins4.hmm globins45.fa minifam.h3i \
>-		Pkinase.hmm fn3.out globins4.out minifam minifam.h3m
>+OPTIONS_DEFINE=	DOCS EXAMPLES TEST
>+TEST_TEST_TARGET=	check
>+TEST_USES=	shebangfix perl5
>+TEST_VARS=	shebang_glob=*.pl shebang_files=easel/devkit/*
> 
>-OPTIONS_DEFINE=	DOCS EXAMPLES
>+DOCFILES=	COPYRIGHT Userguide.pdf
>+EXAMPLES=	7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.out MADE1.sto \
>+		Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.out fn3.sto \
>+		globins4.hmm globins4.out globins4.sto globins45.fa \
>+		minifam minifam.h3f minifam.h3i minifam.h3m minifam.h3p
> 
>-.include <bsd.port.options.mk>
>+.include <bsd.port.pre.mk>
> 
> # HMMER is useless without SSE and any PC in use today should support it
> # Should probably also do enable-vmx on Power processors to enable
>@@ -36,14 +36,17 @@
> CONFIGURE_ARGS+=--enable-sse
> .endif
> 
>+post-build-TEST-on:	do-test
>+
> post-install:
> 	@${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}
> 
>-.include <bsd.port.mk>
>+.include <bsd.port.post.mk>
>Index: distinfo
>===================================================================
>--- distinfo	(revision 453805)
>+++ distinfo	(working copy)
>@@ -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
>Index: pkg-descr
>===================================================================
>--- pkg-descr	(revision 453805)
>+++ pkg-descr	(working copy)
>@@ -7,4 +7,4 @@
> a sequence database to find (and/or align) additional homologues of the
> sequence family.
> 
>-WWW: http://hmmer.janelia.org/
>+WWW: http://hmmer.org/
>Index: pkg-plist
>===================================================================
>--- pkg-plist	(revision 453805)
>+++ pkg-plist	(working copy)
>@@ -1,8 +1,13 @@
>+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
>@@ -9,7 +14,20 @@
> 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
>@@ -16,6 +34,8 @@
> 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
>@@ -22,24 +42,29 @@
> 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%%/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.h3p
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3i
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.hmm
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.out
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.out
>-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam
> %%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3m
>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3p

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Attachments on bug 223561: 187879 | 187888