summaryrefslogtreecommitdiff
path: root/biology
diff options
context:
space:
mode:
Diffstat (limited to 'biology')
-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);\