diff options
author | Johann Visagie <wjv@FreeBSD.org> | 2001-07-05 08:58:12 +0000 |
---|---|---|
committer | Johann Visagie <wjv@FreeBSD.org> | 2001-07-05 08:58:12 +0000 |
commit | 7ddb2910c6aab245ed9a80da93e0819688541461 (patch) | |
tree | 073a14dc5d5f7a89115de7ba33ce423f3808ad12 /biology | |
parent | Update WWW. (diff) |
- General clean-up of port.
- Install PDF and HTML documentation.
- Take over maintainership.
Approved by: Silence from previous maintainer; no objections from -ports
Notes
Notes:
svn path=/head/; revision=44780
Diffstat (limited to 'biology')
-rw-r--r-- | biology/hmmer/Makefile | 19 | ||||
-rw-r--r-- | biology/hmmer/files/patch-Makefile.in | 20 | ||||
-rw-r--r-- | biology/hmmer/pkg-descr | 13 | ||||
-rw-r--r-- | biology/hmmer/pkg-message | 35 | ||||
-rw-r--r-- | biology/hmmer/pkg-plist | 203 |
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 +%%PORTDOCS%%share/doc/hmmer/Userguide.pdf %%PORTDOCS%%share/doc/hmmer/Userguide.ps +%%PORTDOCS%%share/doc/hmmer/hmmer-html/IMG_PARAMS.db +%%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 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