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author | rh <rh> | 1999-07-28 20:07:00 +0000 |
---|---|---|
committer | rh <rh> | 1999-07-28 20:07:00 +0000 |
commit | ba5d0411bab72c896f942b38db3eba75dea14ff8 (patch) | |
tree | 8d105ce7a41bf0c231a758cb3f7d63bab58a989c /biology | |
parent | ff7d310f47831fa503e824419f012e526022c2c8 (diff) | |
download | pkgsrc-ba5d0411bab72c896f942b38db3eba75dea14ff8.tar.gz |
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!
Diffstat (limited to 'biology')
-rw-r--r-- | biology/clustalw/Makefile | 28 | ||||
-rw-r--r-- | biology/clustalw/files/md5 | 3 | ||||
-rw-r--r-- | biology/clustalw/files/patch-sum | 4 | ||||
-rw-r--r-- | biology/clustalw/patches/patch-aa | 13 | ||||
-rw-r--r-- | biology/clustalw/patches/patch-ab | 14 | ||||
-rw-r--r-- | biology/clustalw/pkg/COMMENT | 1 | ||||
-rw-r--r-- | biology/clustalw/pkg/DESCR | 5 | ||||
-rw-r--r-- | biology/clustalw/pkg/MESSAGE | 12 | ||||
-rw-r--r-- | biology/clustalw/pkg/PLIST | 7 |
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 |