- Update port to version 2.2g

4 files changed, 34 insertions, 223 deletions

diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile
index 4259aba6335c..f3c5ead9cd28 100644
--- a/biology/hmmer/Makefile
+++ b/biology/hmmer/Makefile
@@ -6,28 +6,29 @@
 #
 
 PORTNAME=	hmmer
-PORTVERSION=	2.1.1
+PORTVERSION=	2.2.g
 CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/
-EXTRACT_SUFX=	.tar.Z
+MASTER_SITES=	ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/${VERSIONSTRING}/
+DISTNAME=	${PORTNAME}-${VERSIONSTRING}
 
 MAINTAINER=	wjv@FreeBSD.org
 
 GNU_CONFIGURE=	yes
 USE_PERL5=	yes
+VERSIONSTRING=	${PORTVERSION:C|\.([^.]*)$|\1|}
 
-MAN1=		hmmalign.1 hmmbuild.1 hmmcalibrate.1 hmmconvert.1 hmmemit.1 \
-		hmmer.1 hmmpfam.1 hmmsearch.1 hmmfetch.1 hmmindex.1 alistat.1 \
-		getseq.1 seqstat.1 sreformat.1
-
-HMMER_DOCDIR=	${PREFIX}/share/doc/${PORTNAME}
+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
 
 post-install:
 .if !defined(NOPORTDOCS)
-	@ ${MKDIR} ${HMMER_DOCDIR}
-	@ ${INSTALL_DATA} ${WRKSRC}/Userguide/Userguide.pdf ${HMMER_DOCDIR}
-	@ ${INSTALL_DATA} ${WRKSRC}/Userguide/Userguide.ps ${HMMER_DOCDIR}
-	@ ${TAR} xzfC ${WRKSRC}/Userguide/hmmer-html.tar.Z ${HMMER_DOCDIR}
+	@ ${MKDIR} ${DOCSDIR}
+.for docfile in ${DOCFILES}
+	@ ${INSTALL_DATA} ${WRKSRC}/${docfile} ${DOCSDIR}
+.endfor
 .endif
 .if !defined(BATCH)
 	@ ${CAT} ${PKGMESSAGE}
diff --git a/biology/hmmer/distinfo b/biology/hmmer/distinfo
index 6dbe81b02fd8..99b8a3003bed 100644
--- a/biology/hmmer/distinfo
+++ b/biology/hmmer/distinfo
@@ -1 +1 @@
-MD5 (hmmer-2.1.1.tar.Z) = 0f98910a3507b4d52fbe82adc6fa89b5
+MD5 (hmmer-2.2g.tar.gz) = d7def2007a0aaf2eafb9a96a07986b8c
diff --git a/biology/hmmer/files/patch-Makefile.in b/biology/hmmer/files/patch-Makefile.in
index deade1eaceeb..40e1561681b4 100644
--- a/biology/hmmer/files/patch-Makefile.in
+++ b/biology/hmmer/files/patch-Makefile.in
@@ -1,5 +1,5 @@
---- Makefile.in.orig	Thu Dec 10 01:11:07 1998
-+++ Makefile.in	Wed Jul  4 15:41:09 2001
+--- 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.
@@ -9,12 +9,19 @@
  MANSUFFIX = 1
  
  # your compiler and compiler flags
-@@ -142,7 +142,7 @@
- #          installs man pages in MANDIR/man1/  (if MANSUFFIX is 1)
+@@ -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\
- 	   $(INSTMAN) Man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+-	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/pkg-plist b/biology/hmmer/pkg-plist
index 86b1ac45a9be..b633cb15c522 100644
--- a/biology/hmmer/pkg-plist
+++ b/biology/hmmer/pkg-plist
@@ -1,5 +1,5 @@
+bin/afetch
 bin/alistat
-bin/getseq
 bin/hmmalign
 bin/hmmbuild
 bin/hmmcalibrate
@@ -10,209 +10,12 @@ bin/hmmindex
 bin/hmmpfam
 bin/hmmsearch
 bin/seqstat
+bin/sfetch
+bin/shuffle
+bin/sindex
 bin/sreformat
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+%%PORTDOCS%%share/doc/hmmer/NOTES
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