From 8546beeba575e2efc36f5126f12b5b77167a5bdd Mon Sep 17 00:00:00 2001
From: Steve Price <steve@FreeBSD.org>
Date: Mon, 10 Jul 2000 03:17:40 +0000
Subject: Adding clustalw version 1.81. A CLUSTAL W Multiple Sequence Alignment
Program.
PR: 19746
Submitted by: David A. Bader <dbader@cielo.eece.unm.edu>
---
biology/clustalw/Makefile | 26 ++++++++++++++++++++++++++
biology/clustalw/distinfo | 1 +
biology/clustalw/files/patch-aa | 11 +++++++++++
biology/clustalw/pkg-comment | 1 +
biology/clustalw/pkg-descr | 24 ++++++++++++++++++++++++
biology/clustalw/pkg-plist | 3 +++
6 files changed, 66 insertions(+)
create mode 100644 biology/clustalw/Makefile
create mode 100644 biology/clustalw/distinfo
create mode 100644 biology/clustalw/files/patch-aa
create mode 100644 biology/clustalw/pkg-comment
create mode 100644 biology/clustalw/pkg-descr
create mode 100644 biology/clustalw/pkg-plist
(limited to 'biology/clustalw')
diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile
new file mode 100644
index 000000000000..5cedd67f3f54
--- /dev/null
+++ b/biology/clustalw/Makefile
@@ -0,0 +1,26 @@
+# New ports collection makefile for: clustalw
+# Date created: 6 July 2000
+# Whom: dbader@eece.unm.edu
+#
+# $FreeBSD$
+#
+
+PORTNAME= clustalw
+PORTVERSION= 1.81
+CATEGORIES= biology
+MASTER_SITES= ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
+DISTNAME= clustalw1.81.UNIX
+
+MAINTAINER= dbader@eece.unm.edu
+
+WRKSRC= ${WRKDIR}/${PORTNAME}${PORTVERSION}
+
+do-build:
+ cd ${WRKSRC} ; ${MAKE} -f makefile
+
+do-install:
+ ${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${PREFIX}/bin
+ ${MKDIR} ${PREFIX}/share/${PORTNAME}
+ ${INSTALL_DATA} ${WRKSRC}/clustalw_help ${PREFIX}/share/${PORTNAME}
+
+.include <bsd.port.mk>
diff --git a/biology/clustalw/distinfo b/biology/clustalw/distinfo
new file mode 100644
index 000000000000..030d31087b87
--- /dev/null
+++ b/biology/clustalw/distinfo
@@ -0,0 +1 @@
+MD5 (clustalw1.81.UNIX.tar.gz) = f239ed842186606ef62529720655ab99
diff --git a/biology/clustalw/files/patch-aa b/biology/clustalw/files/patch-aa
new file mode 100644
index 000000000000..d404277773d9
--- /dev/null
+++ b/biology/clustalw/files/patch-aa
@@ -0,0 +1,11 @@
+--- clustalw.c-orig Wed Jun 7 01:50:05 2000
++++ clustalw.c Thu Jul 6 20:19:31 2000
+@@ -33,7 +33,7 @@
+ #ifdef MSDOS
+ char *help_file_name = "clustalw.hlp";
+ #else
+- char *help_file_name = "clustalw_help";
++ char *help_file_name = "/usr/local/share/clustalw/clustalw_help";
+ #endif
+
+ sint max_names; /* maximum length of names in current alignment file */
diff --git a/biology/clustalw/pkg-comment b/biology/clustalw/pkg-comment
new file mode 100644
index 000000000000..96dce0a32542
--- /dev/null
+++ b/biology/clustalw/pkg-comment
@@ -0,0 +1 @@
+CLUSTAL W Multiple Sequence Alignment Program
diff --git a/biology/clustalw/pkg-descr b/biology/clustalw/pkg-descr
new file mode 100644
index 000000000000..fcb3931270b0
--- /dev/null
+++ b/biology/clustalw/pkg-descr
@@ -0,0 +1,24 @@
+ CLUSTAL W Multiple Sequence Alignment Program
+
+ClustalW was written by Des Higgins (now at University College, Cork,
+Ireland) (des@chah.ucc.ie), Julie Thompson (julie@IGBMC.u-strasbg.fr),
+Toby Gibson, (Gibson@EMBL-Heidelberg.DE), and Franc'ois Jeanmougin
+(pingouin@igbmc.u-strasbg.fr). It is a complete rewrite and upgrade of
+the Clustal and ClustalV packages. which were developed by Des
+Higgins. New features include the ability to detect read different
+input formats (NBRF/PIR, Fasta, EMBL/Swissprot); align old alignments;
+produce phylogenetic trees after alignment (Neighbor Joining trees
+with a bootstrap option); write different alignment formats (Clustal,
+NBRF/PIR, GCG, PHYLIP); full command line interface. It is described
+in the following papers:
+
+ Thompson, J.D., D. G. Higgins and T. J. Gibson. 1994. CLUSTAL W:
+improving the sensitivity of progressive multiple sequence alignment
+through sequence weighting, positions-specific gap penalties and
+weight matrix choice. Nucleic Acids Research 22: 4673-4680.
+
+ Higgins, D. G., J. D. Thompson, and T. J. Gibson. 1996. Using
+CLUSTAL for multiple sequence alignments. Methods in Enzymology 266:
+383-402.
+
+ See URL: www-igbmc.u-strasbg.fr/BioInfo/ClustalX/Top.html
diff --git a/biology/clustalw/pkg-plist b/biology/clustalw/pkg-plist
new file mode 100644
index 000000000000..32ff2fc3ac77
--- /dev/null
+++ b/biology/clustalw/pkg-plist
@@ -0,0 +1,3 @@
+bin/clustalw
+share/clustalw/clustalw_help
+@dirrm share/clustalw
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