- General clean-up of port.

- Install PDF and HTML documentation.
- Take over maintainership.

Approved by:	Silence from previous maintainer; no objections from -ports

5 files changed, 252 insertions, 38 deletions

diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile
index 6975bba5e95f..4259aba6335c 100644
--- a/biology/hmmer/Makefile
+++ b/biology/hmmer/Makefile
@@ -11,27 +11,26 @@ CATEGORIES=	biology
 MASTER_SITES=	ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/
 EXTRACT_SUFX=	.tar.Z
 
-MAINTAINER=	barnhart@genetics.wustl.edu
+MAINTAINER=	wjv@FreeBSD.org
 
 GNU_CONFIGURE=	yes
-
 USE_PERL5=	yes
+
 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
 
-post-build:
-	@ strip ${WRKSRC}/binaries/*
-	@ make test
-
-test:
-	@(cd ${WRKSRC}; make check)
+HMMER_DOCDIR=	${PREFIX}/share/doc/${PORTNAME}
 
 post-install:
 .if !defined(NOPORTDOCS)
-	${MKDIR} ${PREFIX}/share/doc/hmmer
-	${INSTALL_DATA} ${WRKSRC}/Userguide/Userguide.ps ${PREFIX}/share/doc/hmmer
+	@ ${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}
 .endif
+.if !defined(BATCH)
 	@ ${CAT} ${PKGMESSAGE}
+.endif
 
 .include <bsd.port.mk>
diff --git a/biology/hmmer/files/patch-Makefile.in b/biology/hmmer/files/patch-Makefile.in
new file mode 100644
index 000000000000..deade1eaceeb
--- /dev/null
+++ b/biology/hmmer/files/patch-Makefile.in
@@ -0,0 +1,20 @@
+--- Makefile.in.orig	Thu Dec 10 01:11:07 1998
++++ Makefile.in	Wed Jul  4 15:41:09 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
+@@ -142,7 +142,7 @@
+ #          installs man pages in MANDIR/man1/  (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);\
diff --git a/biology/hmmer/pkg-descr b/biology/hmmer/pkg-descr
index c30abfd4d218..165fcd76b377 100644
--- a/biology/hmmer/pkg-descr
+++ b/biology/hmmer/pkg-descr
@@ -1,9 +1,10 @@
-HMMER is an implementation of profile HMM methods for sensitive database 
-searches using multiple sequence alignments as queries.
+HMMER is an implementation of profile hidden Markov model methods for
+sensitive searches of biological sequence databases using multiple sequence
+alignments as queries.
 
-Basically, you give HMMER a multiple sequence alignment as input; it builds 
-a statistical model called a "hidden Markov model" which you can then use as 
-a query into a sequence database to find (and/or align) additional 
-homologues of the sequence family.
+Given a multiple sequence alignment as input, HMMER builds a statistical
+model called a "hidden Markov model" which can then be used as a query into
+a sequence database to find (and/or align) additional homologues of the
+sequence family.
 
 WWW: http://hmmer.wustl.edu/
diff --git a/biology/hmmer/pkg-message b/biology/hmmer/pkg-message
index dbfd059121b1..08e75304b7e8 100644
--- a/biology/hmmer/pkg-message
+++ b/biology/hmmer/pkg-message
@@ -1,22 +1,13 @@
-*********************************************************
-
-Note on environment variables:
-
-   HMMER reads three environment variables:
-      HMMERDB  - directory location of HMM databases (e.g. PFAM)
-      BLASTDB  - directory location of FASTA-formatted sequence databases
-      BLASTMAT - directory location of PAM scoring matrices
-
-   If you have installed BLAST, you probably already have these 
-   environment variables set in system-wide or user-specific
-   .cshrc files. They are optional. If they are set up, you
-   can simplify command lines to:
-      > hmmpfam pfam my.query
-      > hmmsearch my.hmm swiss35
-   instead of
-      > hmmpfam   /some/long/path/to/databases/pfam my.query
-      > hmmsearch my.hmm /some/long/path/to/databases/swiss35
-
-Please see the website http://hmmer.wustl.edu/ for more information.
-
-*********************************************************
+---------------------------------------------------------------------------
+HMMER reads three optional environment variables:
+  HMMERDB  - directory location of HMM databases (e.g. PFAM)
+  BLASTDB  - directory location of FASTA-formatted sequence databases
+  BLASTMAT - directory location of PAM scoring matrices
+
+The BLASTDB and BLASTMAT variables are shared with versions of BLAST such
+as NCBI BLAST 2.0 (contained in the biology/ncbi-toolkit port).  If these
+variables are set, you do not have to specify the full path to your
+databases on the command line when using HMMER.
+
+Please see the documentation for more information.
+---------------------------------------------------------------------------
diff --git a/biology/hmmer/pkg-plist b/biology/hmmer/pkg-plist
index 81a673fa8731..86b1ac45a9be 100644
--- a/biology/hmmer/pkg-plist
+++ b/biology/hmmer/pkg-plist
@@ -11,5 +11,208 @@ bin/hmmpfam
 bin/hmmsearch
 bin/seqstat
 bin/sreformat
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 %%PORTDOCS%%share/doc/hmmer/Userguide.ps
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+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/ID_MAP.db
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/ORIG_MAP.db
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/aux_preamble
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/dependent
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/depends_on
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/env_style
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/envstyles.db
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/expanded.db
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/global.db
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/main-expanded
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/new_command
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/new_environment
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/new_theorem
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/part001
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/preamble
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/prelatex
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/styleID
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+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/styles
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/txt_style
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/txtstyles.db
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/verb.db
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/verb_delim.db
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/verbatim
+%%PORTDOCS%%share/doc/hmmer/hmmer-html/TMP/verbatim_counter
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+%%PORTDOCS%%share/doc/hmmer/hmmer-html/footnode.html
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