Attachment 48575 Details for Bug 74331 – hmmer.diff

[patch] hmmer.diff

hmmer.diff (text/plain), 5.29 KB, created by Fernan Aguero on 2004-11-24 20:00:45 UTC

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Creator: Fernan Aguero

Created: 2004-11-24 20:00:45 UTC

Size: 5.29 KB

patch

obsolete

>diff -ruN /usr/ports/biology/hmmer/Makefile hmmer/Makefile
>--- /usr/ports/biology/hmmer/Makefile	Mon Nov 22 06:09:09 2004
>+++ hmmer/Makefile	Wed Nov 24 13:30:32 2004
>@@ -6,24 +6,29 @@
> #
> 
> PORTNAME=	hmmer
>-PORTVERSION=	2.2.g
>-PORTREVISION=	1
>+PORTVERSION=	2.3.2
> CATEGORIES=	biology
>-MASTER_SITES=	ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/${VERSIONSTRING}/
>-DISTNAME=	${PORTNAME}-${VERSIONSTRING}
>+MASTER_SITES=	ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/${PORTVERSION}/
> 
>-MAINTAINER=	ports@FreeBSD.org
>+MAINTAINER=	fernan@iib.unsam.edu.ar
> COMMENT=	Profile hidden Markov models for biological sequence analysis
> 
> GNU_CONFIGURE=	yes
> USE_PERL5=	yes
>-VERSIONSTRING=	${PORTVERSION:C|\.([^.]*)$|\1|}
>+CONFIGURE_ARGS+=--enable-threads --enable-lfs
> 
>-DOCFILES=	00README COPYRIGHT NOTES Userguide.pdf
>-MAN1=		afetch.1 alistat.1 hmmalign.1 hmmbuild.1 hmmcalibrate.1 \
>-		hmmconvert.1 hmmemit.1 hmmer.1 hmmfetch.1 hmmindex.1 \
>-		hmmpfam.1 hmmsearch.1 seqstat.1 sfetch.1 shuffle.1 \
>-		sreformat.1
>+DOCFILES=	00README COPYRIGHT INSTALL LICENSE NOTES Userguide.pdf
>+EXAMPLES=	7LES_DROME amino.null globins50.msf nucleic.pri rrm.sto \
>+		Artemia.fa amino.pri globins630.fa pkinase.sto RU1A_HUMAN \
>+		fn3.sto nucleic.null rrm.hmm
>+MAN1=		hmmalign.1 hmmbuild.1 hmmcalibrate.1 hmmconvert.1 hmmemit.1 \
>+		hmmer.1 hmmfetch.1 hmmindex.1 hmmpfam.1 hmmsearch.1 
>+
>+.if defined(WITH_PVM)
>+CONFIGURE_ENV+=		PVM_ROOT="${LOCALBASE}/lib/pvm" PVM_ARCH="FREEBSD"
>+CONFIGURE_ARGS+=	--with-pvm
>+BUILD_DEPENDS+=		pvm:${PORTSDIR}/net/pvm
>+.endif
> 
> post-install:
> .if !defined(NOPORTDOCS)
>@@ -32,6 +37,10 @@
> 	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
> .endfor
> .endif
>+	@ ${MKDIR} ${EXAMPLESDIR}
>+.for example in ${EXAMPLES}
>+	@ ${INSTALL_DATA} ${WRKSRC}/tutorial/${example} ${EXAMPLESDIR}
>+.endfor
> .if !defined(BATCH)
> 	@ ${CAT} ${PKGMESSAGE}
> .endif
>diff -ruN /usr/ports/biology/hmmer/distinfo hmmer/distinfo
>--- /usr/ports/biology/hmmer/distinfo	Sat Apr  3 01:03:36 2004
>+++ hmmer/distinfo	Wed Nov 24 10:05:32 2004
>@@ -1,2 +1,2 @@
>-MD5 (hmmer-2.2g.tar.gz) = d7def2007a0aaf2eafb9a96a07986b8c
>-SIZE (hmmer-2.2g.tar.gz) = 931569
>+MD5 (hmmer-2.3.2.tar.gz) = 5f073340c0cf761288f961a73821228a
>+SIZE (hmmer-2.3.2.tar.gz) = 1024933
>diff -ruN /usr/ports/biology/hmmer/files/patch-Makefile.in hmmer/files/patch-Makefile.in
>--- /usr/ports/biology/hmmer/files/patch-Makefile.in	Wed Aug 22 10:18:10 2001
>+++ hmmer/files/patch-Makefile.in	Wed Dec 31 21:00:00 1969
>@@ -1,27 +0,0 @@
>---- Makefile.in.orig	Mon Aug  6 01:55:36 2001
>-+++ Makefile.in	Wed Aug 22 14:52:30 2001
>-@@ -34,7 +34,7 @@
>- # how to install the man pages; 
>- # cp is generally fine, unless you preformat your pages.
>- #
>--INSTMAN   = cp
>-+INSTMAN   = $(BSD_INSTALL_MAN)
>- MANSUFFIX = 1
>- 
>- # your compiler and compiler flags
>-@@ -144,12 +144,12 @@
>- #          installs man pages in MANDIR/man1/  (e.g. if MANSUFFIX is 1)
>- install: 
>- 	for file in $(PROGS) $(SQUIDPROGS) $(PVMPROGS); do\
>--	   cp binaries/$$file $(BINDIR)/;\
>-+	   $(BSD_INSTALL_PROGRAM) binaries/$$file $(BINDIR)/;\
>- 	done
>--	for file in hmmer $(PROGS) $(SQUIDPROGS); do\
>-+	for file in hmmer $(PROGS); do\
>- 	   $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
>- 	done
>--	for file in $(SQUIDPROGS); do\
>-+	for file in afetch alistat seqstat sfetch shuffle sreformat; do\
>- 	   $(INSTMAN) squid/Man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
>- 	done
>- 
>diff -ruN /usr/ports/biology/hmmer/files/patch-configure hmmer/files/patch-configure
>--- /usr/ports/biology/hmmer/files/patch-configure	Thu Jul 11 07:52:14 2002
>+++ hmmer/files/patch-configure	Wed Dec 31 21:00:00 1969
>@@ -1,22 +0,0 @@
>---- configure.orig	Mon Aug  6 01:55:52 2001
>-+++ configure	Thu Jul 11 12:38:47 2002
>-@@ -1094,6 +1094,9 @@
>- 
>-         acx_pthread_flags="-pthread -pthreads pthread -mt $acx_pthread_flags"
>-         ;;
>-+        *freebsd5*)
>-+	acx_pthread_flags="-lc_r -kthread lthread -pthread"
>-+        ;;
>- esac
>- 
>- if test x"$acx_pthread_ok" = xno; then
>-@@ -1418,6 +1421,9 @@
>-         # we'll just look for -pthreads and -lpthread first:
>- 
>-         acx_pthread_flags="-pthread -pthreads pthread -mt $acx_pthread_flags"
>-+        ;;
>-+        *freebsd5*)
>-+	acx_pthread_flags="-lc_r -kthread lthread -pthread"
>-         ;;
>- esac
>- 
>diff -ruN /usr/ports/biology/hmmer/pkg-plist hmmer/pkg-plist
>--- /usr/ports/biology/hmmer/pkg-plist	Sat Oct 25 01:18:24 2003
>+++ hmmer/pkg-plist	Wed Nov 24 12:04:50 2004
>@@ -1,5 +1,3 @@
>-bin/afetch
>-bin/alistat
> bin/hmmalign
> bin/hmmbuild
> bin/hmmcalibrate
>@@ -9,13 +7,24 @@
> bin/hmmindex
> bin/hmmpfam
> bin/hmmsearch
>-bin/seqstat
>-bin/sfetch
>-bin/shuffle
>-bin/sindex
>-bin/sreformat
>-%%PORTDOCS%%%%DOCSDIR%%/00README
>-%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
>-%%PORTDOCS%%%%DOCSDIR%%/NOTES
>-%%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf
>+%%PORTDOCS%%DOCSDIR%%/00README
>+%%PORTDOCS%%DOCSDIR%%/COPYRIGHT
>+%%PORTDOCS%%DOCSDIR%%/INSTALL
>+%%PORTDOCS%%DOCSDIR%%/LICENSE
>+%%PORTDOCS%%DOCSDIR%%/NOTES
>+%%PORTDOCS%%DOCSDIR%%/Userguide.pdf
>+%%EXAMPLESDIR%%/7LES_DROME
>+%%EXAMPLESDIR%%/amino.null
>+%%EXAMPLESDIR%%/globins50.msf
>+%%EXAMPLESDIR%%/nucleic.pri
>+%%EXAMPLESDIR%%/rrm.sto
>+%%EXAMPLESDIR%%/Artemia.fa
>+%%EXAMPLESDIR%%/amino.pri
>+%%EXAMPLESDIR%%/globins630.fa
>+%%EXAMPLESDIR%%/pkinase.sto
>+%%EXAMPLESDIR%%/RU1A_HUMAN
>+%%EXAMPLESDIR%%/fn3.sto
>+%%EXAMPLESDIR%%/nucleic.null
>+%%EXAMPLESDIR%%/rrm.hmm
> %%PORTDOCS%%@dirrm %%DOCSDIR%%
>+@dirrm %%EXAMPLESDIR%%

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Attachments on bug 74331: 48575