Import of clustalw-1.8, a general purpose multiple alignment program

for DNA or proteins.  This is a merge of the packages submitted in PRs
pkg/7075 by Brook Milligan and pkg/8094 by Marc Baudoin (with some minor
modifications), thanks!

9 files changed, 87 insertions, 0 deletions

diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile
new file mode 100644
index 00000000000..59018b50007
--- /dev/null
+++ b/biology/clustalw/Makefile
@@ -0,0 +1,28 @@
+# $NetBSD: Makefile,v 1.1.1.1 1999/07/28 20:07:00 rh Exp $
+
+DISTNAME=	clustalw1.8.UNIX
+PKGNAME=	clustalw-1.8
+WRKSRC=		${WRKDIR}/clustalw1.8
+CATEGORIES=	biology
+MASTER_SITES=	ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ \
+		ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
+
+MAINTAINER=	babafou@babafou.eu.org
+HOMEPAGE=	http://www-igbmc.u-strasbg.fr/BioInfo/ClustalW/
+
+MAKEFILE=	makefile
+ALL_TARGET=	clustalw
+
+post-patch:
+	@${SED} -e 's:@PREFIX@:${PREFIX}:' < ${WRKSRC}/clustalw.c \
+		> ${WRKSRC}/clustalw.c.tmp \
+		&& ${MV} ${WRKSRC}/clustalw.c.tmp ${WRKSRC}/clustalw.c
+
+do-install:
+	${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${PREFIX}/bin
+	${INSTALL_DATA_DIR} ${PREFIX}/share/doc/clustalw
+	for f in clustalv.doc clustalw.doc clustalw.ms clustalw_help; do \
+		${INSTALL_DATA} ${WRKSRC}/$$f ${PREFIX}/share/doc/clustalw; \
+	done
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/clustalw/files/md5 b/biology/clustalw/files/md5
new file mode 100644
index 00000000000..7336de6a545
--- /dev/null
+++ b/biology/clustalw/files/md5
@@ -0,0 +1,3 @@
+$NetBSD: md5,v 1.1.1.1 1999/07/28 20:07:00 rh Exp $
+
+MD5 (clustalw1.8.UNIX.tar.gz) = 89f55306771e497e614f4bd1206aecea
diff --git a/biology/clustalw/files/patch-sum b/biology/clustalw/files/patch-sum
new file mode 100644
index 00000000000..1ea2bbd9781
--- /dev/null
+++ b/biology/clustalw/files/patch-sum
@@ -0,0 +1,4 @@
+$NetBSD: patch-sum,v 1.1.1.1 1999/07/28 20:07:01 rh Exp $
+
+MD5 (patch-aa) = a1b5cc61cddaba19fb24b3b16ee68748
+MD5 (patch-ab) = 7b829f40c6e807ae78766b6b46d5d12e
diff --git a/biology/clustalw/patches/patch-aa b/biology/clustalw/patches/patch-aa
new file mode 100644
index 00000000000..db1644e8641
--- /dev/null
+++ b/biology/clustalw/patches/patch-aa
@@ -0,0 +1,13 @@
+$NetBSD: patch-aa,v 1.1.1.1 1999/07/28 20:07:01 rh Exp $
+
+--- clustalw.c.orig	Fri Jan 16 04:44:05 1998
++++ clustalw.c	Tue Feb 16 11:58:13 1999
+@@ -33,7 +33,7 @@
+ #ifdef MSDOS
+         char *help_file_name = "clustalw.hlp";
+ #else
+-        char *help_file_name = "clustalw_help";
++        char *help_file_name = "@PREFIX@/share/doc/clustalw/clustalw_help";
+ #endif
+ 
+ sint max_names; /* maximum length of names in current alignment file */
diff --git a/biology/clustalw/patches/patch-ab b/biology/clustalw/patches/patch-ab
new file mode 100644
index 00000000000..30350a74a67
--- /dev/null
+++ b/biology/clustalw/patches/patch-ab
@@ -0,0 +1,14 @@
+$NetBSD: patch-ab,v 1.1.1.1 1999/07/28 20:07:01 rh Exp $
+
+--- amenu.c.orig	Mon Dec  8 08:49:12 1997
++++ amenu.c	Sat Apr 10 22:07:58 1999
+@@ -13,7 +13,9 @@
+ static jmp_buf jmpbuf;
+ #ifndef VMS
+ #ifndef AIX
++#ifndef BADSIG
+ #define BADSIG (void (*)())-1
++#endif
+ #endif
+ #endif
+ 
diff --git a/biology/clustalw/pkg/COMMENT b/biology/clustalw/pkg/COMMENT
new file mode 100644
index 00000000000..3261489a144
--- /dev/null
+++ b/biology/clustalw/pkg/COMMENT
@@ -0,0 +1 @@
+General purpose multiple alignment program for DNA or proteins
diff --git a/biology/clustalw/pkg/DESCR b/biology/clustalw/pkg/DESCR
new file mode 100644
index 00000000000..b3ee91c83c2
--- /dev/null
+++ b/biology/clustalw/pkg/DESCR
@@ -0,0 +1,5 @@
+  Clustal W is a general purpose multiple alignment program for
+DNA or proteins.  Clustal W can write various output files in
+Phylip format.  Furthermore, Clustal W is capable of producing
+phylogenetic trees from multiple sequence alignments in the GCG
+MSF Format. 
diff --git a/biology/clustalw/pkg/MESSAGE b/biology/clustalw/pkg/MESSAGE
new file mode 100644
index 00000000000..404802cfc24
--- /dev/null
+++ b/biology/clustalw/pkg/MESSAGE
@@ -0,0 +1,12 @@
+                  POLICY ON COMMERCIAL DISTRIBUTION OF CLUSTAL W
+
+Clustal W is freely available to the user community. However, Clustal W is
+increasingly being distributed as part of commercial sequence analysis
+packages. To help us safeguard future maintenance and development, commercial
+distributors of Clustal W must take out a NON-EXCLUSIVE LICENCE. Anyone
+wishing to commercially distribute version 1.8 of Clustal W should contact the
+authors unless they have previously taken out a licence.
+
+        gibson@embl-heidelberg.de
+        thompson@embl-heidelberg.de
+        d.higgins@ucc.ie
diff --git a/biology/clustalw/pkg/PLIST b/biology/clustalw/pkg/PLIST
new file mode 100644
index 00000000000..638f7811682
--- /dev/null
+++ b/biology/clustalw/pkg/PLIST
@@ -0,0 +1,7 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 1999/07/28 20:07:01 rh Exp $
+bin/clustalw
+share/doc/clustalw/clustalv.doc
+share/doc/clustalw/clustalw.doc
+share/doc/clustalw/clustalw.ms
+share/doc/clustalw/clustalw_help
+@dirrm share/doc/clustalw