5 files changed, 38 insertions, 69 deletions

diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile
index f3e4aa53ce80..c4e8f4a422ac 100644
--- a/biology/hmmer/Makefile
+++ b/biology/hmmer/Makefile
@@ -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 @@ post-install:
 	@ ${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 --git a/biology/hmmer/distinfo b/biology/hmmer/distinfo
index 5df2649917e7..9019d9a8830c 100644
--- a/biology/hmmer/distinfo
+++ b/biology/hmmer/distinfo
@@ -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 --git a/biology/hmmer/files/patch-Makefile.in b/biology/hmmer/files/patch-Makefile.in
deleted file mode 100644
index 40e1561681b4..000000000000
--- a/biology/hmmer/files/patch-Makefile.in
+++ /dev/null
@@ -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 --git a/biology/hmmer/files/patch-configure b/biology/hmmer/files/patch-configure
deleted file mode 100644
index 495beac9e357..000000000000
--- a/biology/hmmer/files/patch-configure
+++ /dev/null
@@ -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 --git a/biology/hmmer/pkg-plist b/biology/hmmer/pkg-plist
index 52a347da357a..27a07b38ee15 100644
--- a/biology/hmmer/pkg-plist
+++ b/biology/hmmer/pkg-plist
@@ -1,5 +1,3 @@
-bin/afetch
-bin/alistat
 bin/hmmalign
 bin/hmmbuild
 bin/hmmcalibrate
@@ -9,13 +7,24 @@ bin/hmmfetch
 bin/hmmindex
 bin/hmmpfam
 bin/hmmsearch
-bin/seqstat
-bin/sfetch
-bin/shuffle
-bin/sindex
-bin/sreformat
 %%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%%