[pkgsrc/trunk]: pkgsrc/biology/hmmer Initial import of hmmer, one of the man...

[jschauma <jschauma%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/62cd9818d049
branches:  trunk
changeset: 462068:62cd9818d049
user:      jschauma <jschauma%pkgsrc.org@localhost>
date:      Fri Sep 26 03:52:47 2003 +0000

description:
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:

 biology/hmmer/DESCR            |   6 ++++++
 biology/hmmer/Makefile         |  16 ++++++++++++++++
 biology/hmmer/PLIST            |  20 ++++++++++++++++++++
 biology/hmmer/distinfo         |   5 +++++
 biology/hmmer/patches/patch-aa |  27 +++++++++++++++++++++++++++
 5 files changed, 74 insertions(+), 0 deletions(-)

diffs (94 lines):

diff -r 8ca05c888618 -r 62cd9818d049 biology/hmmer/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/hmmer/DESCR       Fri Sep 26 03:52:47 2003 +0000
@@ -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 -r 8ca05c888618 -r 62cd9818d049 biology/hmmer/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/hmmer/Makefile    Fri Sep 26 03:52:47 2003 +0000
@@ -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@localhost
+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 -r 8ca05c888618 -r 62cd9818d049 biology/hmmer/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/hmmer/PLIST       Fri Sep 26 03:52:47 2003 +0000
@@ -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 -r 8ca05c888618 -r 62cd9818d049 biology/hmmer/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/hmmer/distinfo    Fri Sep 26 03:52:47 2003 +0000
@@ -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 -r 8ca05c888618 -r 62cd9818d049 biology/hmmer/patches/patch-aa
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/hmmer/patches/patch-aa    Fri Sep 26 03:52:47 2003 +0000
@@ -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);\