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| author | jschauma <jschauma@pkgsrc.org> | 2003-09-26 03:52:47 +0000 |
|---|---|---|
| committer | jschauma <jschauma@pkgsrc.org> | 2003-09-26 03:52:47 +0000 |
| commit | 20bf40599b88d4fcd6fe9a6008b34f2ddc22a9c1 (patch) | |
| tree | 218097c09ee71f732d2d35ca7025d859a19f9758 /biology/hmmer | |
| parent | b94fb679874887744925d33fe0c78dcb5fa09fd9 (diff) | |
| download | pkgsrc-20bf40599b88d4fcd6fe9a6008b34f2ddc22a9c1.tar.gz | |
Initial import of hmmer, one of the many packages provided by
brook at biology dot nmsu dot edu and his team at NMSU.
HMMER is an implementation of profile HMM methods for sensitive database
searches using multiple sequence alignments as queries. HMMER takes
multiple sequence alignement as input and builds statistical model
called "Hidden Markov Model" which can be used as a query into a
sequence database to find and/or align additional homologues of the
sequence family.
Diffstat (limited to 'biology/hmmer')
| -rw-r--r-- | biology/hmmer/DESCR | 6 | ||||
| -rw-r--r-- | biology/hmmer/Makefile | 16 | ||||
| -rw-r--r-- | biology/hmmer/PLIST | 20 | ||||
| -rw-r--r-- | biology/hmmer/distinfo | 5 | ||||
| -rw-r--r-- | biology/hmmer/patches/patch-aa | 27 |
5 files changed, 74 insertions, 0 deletions
diff --git a/biology/hmmer/DESCR b/biology/hmmer/DESCR new file mode 100644 index 00000000000..fe451f2ada7 --- /dev/null +++ b/biology/hmmer/DESCR @@ -0,0 +1,6 @@ +HMMER is an implementation of profile HMM methods for sensitive database +searches using multiple sequence alignments as queries. HMMER takes +multiple sequence alignement as input and builds statistical model +called "Hidden Markov Model" which can be used as a query into a +sequence database to find and/or align additional homologues of the +sequence family. diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile new file mode 100644 index 00000000000..db1c4d7d724 --- /dev/null +++ b/biology/hmmer/Makefile @@ -0,0 +1,16 @@ +# $NetBSD: Makefile,v 1.1.1.1 2003/09/26 03:52:47 jschauma Exp $ +# + +DISTNAME= hmmer-2.3.1 +WRKSRC= ${WRKDIR}/hmmer-2.3.1 +CATEGORIES= biology +MASTER_SITES= ftp://ftp.genetics.wustl.edu/pub/eddy/hmmer/2.3.1/ + +MAINTAINER= hdp@cs.nmsu.edu +HOMEPAGE= http://hmmer.wustl.edu +COMMENT= Implementation of profile HMM software for protein sequence analysis + +USE_BUILDLINK2= yes +GNU_CONFIGURE= yes + +.include "../../mk/bsd.pkg.mk" diff --git a/biology/hmmer/PLIST b/biology/hmmer/PLIST new file mode 100644 index 00000000000..5dd1779c36a --- /dev/null +++ b/biology/hmmer/PLIST @@ -0,0 +1,20 @@ +@comment $NetBSD: PLIST,v 1.1.1.1 2003/09/26 03:52:47 jschauma Exp $ +bin/hmmalign +bin/hmmbuild +bin/hmmcalibrate +bin/hmmconvert +bin/hmmemit +bin/hmmfetch +bin/hmmindex +bin/hmmpfam +bin/hmmsearch +man/man1/hmmalign.1 +man/man1/hmmbuild.1 +man/man1/hmmcalibrate.1 +man/man1/hmmconvert.1 +man/man1/hmmemit.1 +man/man1/hmmer.1 +man/man1/hmmfetch.1 +man/man1/hmmindex.1 +man/man1/hmmpfam.1 +man/man1/hmmsearch.1 diff --git a/biology/hmmer/distinfo b/biology/hmmer/distinfo new file mode 100644 index 00000000000..81045d8f3ec --- /dev/null +++ b/biology/hmmer/distinfo @@ -0,0 +1,5 @@ +$NetBSD: distinfo,v 1.1.1.1 2003/09/26 03:52:47 jschauma Exp $ + +SHA1 (hmmer-2.3.1.tar.gz) = bf6a3ec56c24332d7e66d6ce8865de1d72dce01f +Size (hmmer-2.3.1.tar.gz) = 1023122 bytes +SHA1 (patch-aa) = c5aa41137bb339a584948b6dc88317c98b4ff6fd diff --git a/biology/hmmer/patches/patch-aa b/biology/hmmer/patches/patch-aa new file mode 100644 index 00000000000..08716d03d06 --- /dev/null +++ b/biology/hmmer/patches/patch-aa @@ -0,0 +1,27 @@ +$NetBSD: patch-aa,v 1.1.1.1 2003/09/26 03:52:47 jschauma Exp $ + +--- Makefile.in.orig 2003-06-13 17:05:13.000000000 -0400 ++++ Makefile.in 2003-09-25 23:47:27.000000000 -0400 +@@ -30,11 +30,12 @@ + exec_prefix = @exec_prefix@ + BINDIR = @bindir@ + MANDIR = @mandir@ ++INSTBIN = ${BSD_INSTALL_PROGRAM} + + # 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 +@@ -112,7 +113,7 @@ + mkdir -p ${BINDIR} + -mkdir -p ${MANDIR}/man${MANSUFFIX} + for file in $(PROGS) $(PVMPROGS); do\ +- cp src/$$file $(BINDIR)/;\ ++ $(INSTBIN) src/$$file $(BINDIR)/;\ + done + -for file in hmmer $(PROGS); do\ + $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\ |