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pkgsrc/biology/mummer/Makefile

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Bump all packages for perl-5.18, that a) refer 'perl' in their Makefile, or b) have a directory name of p5-*, or c) have any dependency on any p5-* package Like last time, where this caused no complaints.
2013-05-31 14:39:35 +02:00
# $NetBSD: Makefile,v 1.21 2013/05/31 12:39:39 wiz Exp $
Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
2003-09-28 00:24:56 +02:00
#
updated to MUMmer3.20
2008-10-12 00:01:13 +02:00
DISTNAME= MUMmer3.20
PKGNAME= mummer-3.20
Bump all packages for perl-5.18, that a) refer 'perl' in their Makefile, or b) have a directory name of p5-*, or c) have any dependency on any p5-* package Like last time, where this caused no complaints.
2013-05-31 14:39:35 +02:00
PKGREVISION= 2
Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
2003-09-28 00:24:56 +02:00
CATEGORIES= biology
Updated biology/mummer to release 3.18. Changes include: - MUMmer now resides at Sourceforge - new tools such as delta-filter - more extensive html documentation and examples - bug fixes
2006-01-29 20:31:43 +01:00
MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=mummer/}
Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
2003-09-28 00:24:56 +02:00
MAINTAINER= hdp@cs.nmsu.edu
Updated biology/mummer to release 3.18. Changes include: - MUMmer now resides at Sourceforge - new tools such as delta-filter - more extensive html documentation and examples - bug fixes
2006-01-29 20:31:43 +01:00
HOMEPAGE= http://mummer.sourceforge.net/
Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
2003-09-28 00:24:56 +02:00
COMMENT= System for aligning whole genome sequences
Move WRKSRC definition away from the first paragraph in a Makefile.
2004-01-20 13:07:06 +01:00
WRKSRC= ${WRKDIR}/${DISTNAME}
Explicitly add pax dependency in those Makefiles that use it (or have patches to add it). Drop pax from the default USE_TOOLS list. Make bsdtar the default for those places that wanted gtar to extract long links etc, as bsdtar can be built of the tree.
2008-05-25 23:42:20 +02:00
USE_TOOLS+= csh:run gmake perl:run pax
Updated biology/mummer to release 3.18. Changes include: - MUMmer now resides at Sourceforge - new tools such as delta-filter - more extensive html documentation and examples - bug fixes
2006-01-29 20:31:43 +01:00
USE_LANGUAGES= c c++
Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
2003-09-28 00:24:56 +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_ENV+= SH=${SH:Q}
MAKE_ENV+= PERL=${PERL5:Q}
Fix path to csh in scripts. Bump revision.
2006-12-06 17:52:20 +01:00
MAKE_ENV+= CSH=${TOOLS_PATH.csh:Q}
Updated mummer to 3.19. Changes since 3.18: - More documentation.
2007-01-18 20:13:10 +01:00
INSTALLATION_DIRS= bin share/doc/mummer share/mummer
Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
2003-09-28 00:24:56 +02:00
do-install:
Updated mummer to 3.19. Changes since 3.18: - More documentation.
2007-01-18 20:13:10 +01:00
.for p in annotate combineMUMs delta-filter gaps mgaps mummer \
Updated biology/mummer to release 3.18. Changes include: - MUMmer now resides at Sourceforge - new tools such as delta-filter - more extensive html documentation and examples - bug fixes
2006-01-29 20:31:43 +01:00
repeat-match show-aligns show-coords show-snps show-tiling
Mechanical changes to add full DESTDIR support to packages that install their files via a custom do-install target.
2008-03-03 01:51:43 +01:00
${INSTALL_PROGRAM} ${WRKSRC}/${p} ${DESTDIR}${PREFIX}/bin
Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
2003-09-28 00:24:56 +02:00
.endfor
Updated mummer to 3.19. Changes since 3.18: - More documentation.
2007-01-18 20:13:10 +01:00
.for p in postnuc postpro prenuc prepro
Mechanical changes to add full DESTDIR support to packages that install their files via a custom do-install target.
2008-03-03 01:51:43 +01:00
${INSTALL_PROGRAM} ${WRKSRC}/aux_bin/${p} ${DESTDIR}${PREFIX}/bin
Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
2003-09-28 00:24:56 +02:00
.endfor
Updated mummer to 3.19. Changes since 3.18: - More documentation.
2007-01-18 20:13:10 +01:00
.for f in run-mummer1 run-mummer3 nucmer promer exact-tandems \
updated to MUMmer3.20
2008-10-12 00:01:13 +02:00
mapview mummerplot nucmer2xfig dnadiff
Mechanical changes to add full DESTDIR support to packages that install their files via a custom do-install target.
2008-03-03 01:51:43 +01:00
${INSTALL_SCRIPT} ${WRKSRC}/${f} ${DESTDIR}${PREFIX}/share/mummer
Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
2003-09-28 00:24:56 +02:00
.endfor
Mechanical changes to add full DESTDIR support to packages that install their files via a custom do-install target.
2008-03-03 01:51:43 +01:00
cd ${WRKSRC}/docs && pax -wr -s ',^Makefile$$,,' * \
${DESTDIR}${PREFIX}/share/doc/mummer
Initial import of mummer, one of the many packages provided by brook at biology dot nmsu dot edu and his team at NMSU. Mummer is a system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides whether in complete or draft form. MUMmer can also align incomplete genomes; it handles the 100s or 1000s of contigs from a shotgun sequencing project with ease, and will align them to another set of contigs or a genome using the NUCmer program included with the system.
2003-09-28 00:24:56 +02:00
.include "../../mk/bsd.pkg.mk"
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