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pkgsrc/biology/clustalw/Makefile

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Update MASTER_SITES and/or HOMEPAGE, from Sergey Svishchev.
2006-10-04 22:46:42 +02:00
# $NetBSD: Makefile,v 1.10 2006/10/04 20:47:03 wiz Exp $
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!
1999-07-28 22:07:00 +02:00
Update to clustalw 1.83. Changes since 1.8 include: * The FASTA format has been added to the list of alignment output options. * It is now possible to save the residue ranges (appended after the sequence names) when saving a specified range of the alignment. * The efficiency of the neighour-joining algorithm has been improved. This work was done by Tadashi Koike at the Center for Information Biology and DNA Data Bank of Japan and FUJITSU Limited. Some example speedups are given below : (timings on a SPARC64 CPU) No. of sequences original NJ new NJ 200 0' 12" 0.1" 500 9' 19" 1.4" 1000 XXXX 0' 31" * ClustalW now returns error codes for some common errors when exiting. This may be useful for people who run clustalw automatically from within a script. Error codes are: 1 bad command line option 2 cannot open sequence file 3 wrong format in sequence file 4 sequence file contains only 1 sequence (for multiple alignments) * Alignments can now be saved in Nexus format, for compatibility with PAUP, MacClade etc. For a description of the Nexus format, see: Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997. NEXUS: an extensible file format for systematic information. Systematic Biology 46:590-621. * Phylogenetic trees can also be saved in nexus format. * A ClustalW icon has been designed for MAC and PC systems.
2004-08-17 01:34:58 +02:00
DISTNAME= clustalw1.83.UNIX
PKGNAME= clustalw-1.83
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!
1999-07-28 22:07:00 +02:00
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
Update MASTER_SITES and/or HOMEPAGE, from Sergey Svishchev.
2006-10-04 22:46:42 +02:00
HOMEPAGE= http://bips.u-strasbg.fr/fr/Documentation/ClustalW/
Update to new COMMENT style: COMMENT var in Makefile instead of pkg/COMMENT.
2001-02-16 14:41:26 +01:00
COMMENT= General purpose multiple alignment program for DNA or proteins
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!
1999-07-28 22:07:00 +02:00
Enable pkgviews installation.
2005-04-19 17:42:49 +02:00
PKG_INSTALLATION_TYPES= overwrite pkgviews
Rename variable MAKEFILE to MAKE_FILE.
2006-09-09 04:41:53 +02:00
MAKE_FILE= makefile
Rename ALL_TARGET to BUILD_TARGET for consistency with other *_TARGETs. Suggested by Roland Illig, ok'd by various.
2004-12-03 16:14:50 +01:00
BUILD_TARGET= clustalw
Update to clustalw 1.83. Changes since 1.8 include: * The FASTA format has been added to the list of alignment output options. * It is now possible to save the residue ranges (appended after the sequence names) when saving a specified range of the alignment. * The efficiency of the neighour-joining algorithm has been improved. This work was done by Tadashi Koike at the Center for Information Biology and DNA Data Bank of Japan and FUJITSU Limited. Some example speedups are given below : (timings on a SPARC64 CPU) No. of sequences original NJ new NJ 200 0' 12" 0.1" 500 9' 19" 1.4" 1000 XXXX 0' 31" * ClustalW now returns error codes for some common errors when exiting. This may be useful for people who run clustalw automatically from within a script. Error codes are: 1 bad command line option 2 cannot open sequence file 3 wrong format in sequence file 4 sequence file contains only 1 sequence (for multiple alignments) * Alignments can now be saved in Nexus format, for compatibility with PAUP, MacClade etc. For a description of the Nexus format, see: Maddison, D. R., D. L. Swofford and W. P. Maddison. 1997. NEXUS: an extensible file format for systematic information. Systematic Biology 46:590-621. * Phylogenetic trees can also be saved in nexus format. * A ClustalW icon has been designed for MAC and PC systems.
2004-08-17 01:34:58 +02:00
WRKSRC= ${WRKDIR}/clustalw1.83
Import of clustalw-1.8, a general purpose multiple alignment program for DNA or proteins. This is a merge of the packages submitted in PRs pkg/7075 by Brook Milligan and pkg/8094 by Marc Baudoin (with some minor modifications), thanks!
1999-07-28 22:07:00 +02:00
Fixed pkglint warnings. The warnings are mostly quoting issues, for example MAKE_ENV+=FOO=${BAR} is changed to MAKE_ENV+=FOO=${BAR:Q}. Some other changes are outlined in http://mail-index.netbsd.org/tech-pkg/2005/12/02/0034.html
2005-12-05 21:49:47 +01:00
MAKE_FLAGS+= CC=${CC:Q}
make sure we use ${CC}.
2004-01-29 14:34:24 +01:00
Enable pkgviews installation.
2005-04-19 17:42:49 +02:00
INSTALLATION_DIRS= bin
Import of clustalw-1.8, a general purpose multiple alignment program for DNA or proteins. This is a merge of the packages submitted in PRs pkg/7075 by Brook Milligan and pkg/8094 by Marc Baudoin (with some minor modifications), thanks!
1999-07-28 22:07:00 +02:00
post-patch:
@${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"
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