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authorjschauma <jschauma@pkgsrc.org>2003-09-26 03:52:47 +0000
committerjschauma <jschauma@pkgsrc.org>2003-09-26 03:52:47 +0000
commit20bf40599b88d4fcd6fe9a6008b34f2ddc22a9c1 (patch)
tree218097c09ee71f732d2d35ca7025d859a19f9758 /biology/hmmer
parentb94fb679874887744925d33fe0c78dcb5fa09fd9 (diff)
downloadpkgsrc-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/DESCR6
-rw-r--r--biology/hmmer/Makefile16
-rw-r--r--biology/hmmer/PLIST20
-rw-r--r--biology/hmmer/distinfo5
-rw-r--r--biology/hmmer/patches/patch-aa27
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);\