ports/74331: update biology/hmmer and take maintainership

Wed Nov 24 20:00:46 UTC 2004

>Number:         74331
>Category:       ports
>Synopsis:       update biology/hmmer and take maintainership
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          update
>Submitter-Id:   current-users
>Arrival-Date:   Wed Nov 24 20:00:45 GMT 2004
>Closed-Date:
>Last-Modified:
>Originator:     Fernan Aguero
>Release:        FreeBSD 4.10-RELEASE i386
>Organization:
IIB-UNSAM
>Environment:

FreeBSD pi.iib.unsam.edu.ar 4.10-RELEASE FreeBSD 4.10-RELEASE #0: Wed May 26 12:56:43 ART 2004 fernan at pi.iib.unsam.edu.ar:/usr/obj/usr/src/sys/PI  i386

	
>Description:
	

	Update HMMER to the latest available version.
	
	While here, add an option (WITH_PVM) so that cluster users can build
	hmmer with pvm support.

	CONFIGURE_ARGS have been set to the defaults used by the software
	authors (see http://hmmer.wustl.edu/#download). This includes enabling
	threads by default. On my FreeBSD-4.10 builds do fine. 
	
	I have not tested this under 5.x myself. However, it appears that the
	thread checks in ${WRKSRC}/configure have been rewritten. 
	I cannot judge if this will work in 5.x, though, due to my limited
	knowledge of this issue and my lack of experience with 5.x

	But I'm sure that any fellow committer reading this can do better than
	me at it :)  (look for 'FreeBSD' within the file)
	
>How-To-Repeat:
	
	
>Fix:

--- hmmer.diff begins here ---
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 at FreeBSD.org
+MAINTAINER=	fernan at 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%%
+ at dirrm %%EXAMPLESDIR%%
--- hmmer.diff ends here ---

>Release-Note:
>Audit-Trail:
>Unformatted:

