diff options
| -rw-r--r-- | biology/clustalw/MESSAGE | 18 | ||||
| -rw-r--r-- | biology/clustalw/Makefile | 30 | ||||
| -rw-r--r-- | biology/clustalw/PLIST | 8 | ||||
| -rw-r--r-- | biology/clustalw/distinfo | 11 | ||||
| -rw-r--r-- | biology/clustalw/patches/patch-aa | 13 | ||||
| -rw-r--r-- | biology/clustalw/patches/patch-ab | 14 | ||||
| -rw-r--r-- | biology/clustalw/patches/patch-interface.c | 13 |
7 files changed, 13 insertions, 94 deletions
diff --git a/biology/clustalw/MESSAGE b/biology/clustalw/MESSAGE deleted file mode 100644 index 77eb1381117..00000000000 --- a/biology/clustalw/MESSAGE +++ /dev/null @@ -1,18 +0,0 @@ -=========================================================================== -$NetBSD: MESSAGE,v 1.3 2004/08/16 23:34:58 ben Exp $ - -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 1.83 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/Makefile b/biology/clustalw/Makefile index 4899a7c60ab..df0c9789f33 100644 --- a/biology/clustalw/Makefile +++ b/biology/clustalw/Makefile @@ -1,36 +1,20 @@ -# $NetBSD: Makefile,v 1.12 2012/09/11 20:32:11 asau Exp $ +# $NetBSD: Makefile,v 1.13 2012/12/13 13:27:13 wen Exp $ -DISTNAME= clustalw1.83.UNIX -PKGNAME= clustalw-1.83 +DISTNAME= clustalw-2.1 CATEGORIES= biology -MASTER_SITES= ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ \ - ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/ +MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.1/ \ + http://www.clustal.org/download/current/ MAINTAINER= babafou@babafou.eu.org HOMEPAGE= http://bips.u-strasbg.fr/fr/Documentation/ClustalW/ COMMENT= General purpose multiple alignment program for DNA or proteins +LICENSE= gnu-gpl-v3 AND gnu-lgpl-v3 PKG_INSTALLATION_TYPES= overwrite pkgviews -MAKE_FILE= makefile -BUILD_TARGET= clustalw -WRKSRC= ${WRKDIR}/clustalw1.83 - -MAKE_FLAGS+= CC=${CC:Q} +GNU_CONFIGURE= yes +USE_LANGUAGES= c c++ INSTALLATION_DIRS= bin -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 ${DESTDIR}${PREFIX}/bin - ${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/clustalw - for f in clustalv.doc clustalw.doc clustalw.ms clustalw_help; do \ - ${INSTALL_DATA} ${WRKSRC}/$$f \ - ${DESTDIR}${PREFIX}/share/doc/clustalw; \ - done - .include "../../mk/bsd.pkg.mk" diff --git a/biology/clustalw/PLIST b/biology/clustalw/PLIST index 637727a70be..674a7a77ec4 100644 --- a/biology/clustalw/PLIST +++ b/biology/clustalw/PLIST @@ -1,6 +1,2 @@ -@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $ -bin/clustalw -share/doc/clustalw/clustalv.doc -share/doc/clustalw/clustalw.doc -share/doc/clustalw/clustalw.ms -share/doc/clustalw/clustalw_help +@comment $NetBSD: PLIST,v 1.3 2012/12/13 13:27:13 wen Exp $ +bin/clustalw2 diff --git a/biology/clustalw/distinfo b/biology/clustalw/distinfo index d1f33f6da92..23a17aaae23 100644 --- a/biology/clustalw/distinfo +++ b/biology/clustalw/distinfo @@ -1,8 +1,5 @@ -$NetBSD: distinfo,v 1.5 2012/10/20 22:02:07 joerg Exp $ +$NetBSD: distinfo,v 1.6 2012/12/13 13:27:13 wen Exp $ -SHA1 (clustalw1.83.UNIX.tar.gz) = 801ce911749171471b7964a1cff93c53c876c282 -RMD160 (clustalw1.83.UNIX.tar.gz) = 20c0ec7739be6747ae08220e5abf2bae412f039e -Size (clustalw1.83.UNIX.tar.gz) = 166863 bytes -SHA1 (patch-aa) = 96f95acb4a312c96440275ca65f7f908c9b9032f -SHA1 (patch-ab) = 75fb21b88132bdf18e7f6bc13d1d35051a1babea -SHA1 (patch-interface.c) = 4c5f76efee503d55aafec87edcb5cbb40f71579d +SHA1 (clustalw-2.1.tar.gz) = f29784f68585544baa77cbeca6392e533d4cf433 +RMD160 (clustalw-2.1.tar.gz) = e193769955a6270797fcb039ca398a4b59d9248d +Size (clustalw-2.1.tar.gz) = 350761 bytes diff --git a/biology/clustalw/patches/patch-aa b/biology/clustalw/patches/patch-aa deleted file mode 100644 index db1644e8641..00000000000 --- a/biology/clustalw/patches/patch-aa +++ /dev/null @@ -1,13 +0,0 @@ -$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 deleted file mode 100644 index 30350a74a67..00000000000 --- a/biology/clustalw/patches/patch-ab +++ /dev/null @@ -1,14 +0,0 @@ -$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/patches/patch-interface.c b/biology/clustalw/patches/patch-interface.c deleted file mode 100644 index f1666bda383..00000000000 --- a/biology/clustalw/patches/patch-interface.c +++ /dev/null @@ -1,13 +0,0 @@ -$NetBSD: patch-interface.c,v 1.1 2012/10/20 22:02:07 joerg Exp $ - ---- interface.c.orig 2012-10-20 14:27:11.000000000 +0000 -+++ interface.c -@@ -210,7 +210,7 @@ static sint check_param(char **args,char - Boolean name1 = FALSE; - sint ajb; - -- if(args[0]==NULL) return; -+ if(args[0]==NULL) return -1; - - - |