pkgsrc - [no description]

Age	Commit message (Collapse)	Author	Files	Lines
2008-10-11	updated to MUMmer3.20	schwarz	5	-45/+25

2008-05-25	Explicitly add pax dependency in those Makefiles that use it (or have	joerg	1	-2/+2
	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.
2008-03-03	Mechanical changes to add full DESTDIR support to packages that install	jlam	1	-5/+8
	their files via a custom do-install target.
2007-01-18	Updated mummer to 3.19.	rillig	4	-128/+91
	Changes since 3.18: - More documentation.
2006-12-06	Fix path to csh in scripts. Bump revision.	joerg	4	-12/+16

2006-06-21	Add csh:run to USE_TOOLS because this package installs csh scripts.	minskim	1	-3/+3
	Bump PKGREVISION.
2006-06-21	Reorder dirrm@'s so that the package is deinstalled propertly.	minskim	1	-4/+4
	PKGREVISION will be bumped with another change shortly.
2006-04-19	Fix build with newer versions of GNU make.	joerg	2	-1/+25

2006-02-05	Recursive revision bump / recommended bump for gettext ABI change.	joerg	1	-1/+2

2006-01-29	Updated biology/mummer to release 3.18. Changes include:	schwarz	5	-32/+134
	- MUMmer now resides at Sourceforge - new tools such as delta-filter - more extensive html documentation and examples - bug fixes
2005-12-05	Fixed pkglint warnings. The warnings are mostly quoting issues, for	rillig	1	-3/+3
	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
2005-07-16	Remove some unnecessarily strong dependencies on perl that resulted	jlam	1	-3/+2
	from including perl5/buildlink3.mk. These packages just need the Perl interpreter, and can just add "perl" to USE_TOOLS instead.
2005-06-19	Prevent paths to the build directories from being included in the package.	kristerw	3	-2/+18
	Bump PKGREVISION.
2005-06-16	Create directories before installing files into them.	jlam	1	-1/+2

2005-05-23	Removed trailing white-space.	rillig	1	-1/+1

2005-05-22	Remove USE_GNU_TOOLS and replace with the correct USE_TOOLS definitions:	jlam	1	-2/+2
	USE_GNU_TOOLS -> USE_TOOLS awk -> gawk m4 -> gm4 make -> gmake sed -> gsed yacc -> bison
2005-04-11	Remove USE_BUILDLINK3 and NO_BUILDLINK; these are no longer used.	tv	1	-2/+1

2005-02-22	Add RMD160 digests in addition to the SHA1 ones.	agc	1	-1/+2

2004-12-05	Update to version 3.15. From David Price in PR#28305.	cube	4	-13/+12
	3.05 - Added -k option to show-coords to only display the best frame for overlapping PROmer alignments. Added --[no]optimize option to nucmer and promer to allow alignment score optimization to be turned off, i.e allow alignments to extend to the ends of sequences rather than backtracking to optimize the alignment score. Updated docs. 3.06 - Added -F and -h option to mummer. Changed -mumcand option to -mumreference, but left deprecated -mumcand option available. Added -maxmatch option to mummer, and changed default behavior of all applicable programs to -mumreference (nucmer, promer and mummer). Added -w (screen width) option to show-aligns. Updated documentation with all of these changes. 3.07 - Added the 'mapview' plotting utility and appropriate documentation. Fixed origin wrap shadowing bug in show-tiling when using the -c option. NUCmer and PROmer now convert to absolute paths to avoid ambiguity. 3.08 - Added MUMmer examples web docs which gives brief walkthroughs 3.10 - Now Mac OSX compatible. Added -R option to show-tiling. 3.11 - Fixed bug show-tiling -R option. Added some mapview changes. Fixed the issue with mummerplot being to faint. 3.12 - Added the --nosimplify option to nucmer for repeat searching. Fixed a bug in nucmer and promer. Fixed rounding issue in show-coords. Updated citations. 3.13 - Added -d, -g, -G and -o options to show-coords and updated documentation. Fixed bug in show-tiling -R 3.14 - Fixed gcc3 compilation bug 3.15 - Fixed --nooptimize in nuc/promer.
2004-04-11	Convert to buildlink3.	snj	1	-3/+3

2004-01-20	Move WRKSRC definition away from the first paragraph in a Makefile.	agc	1	-2/+2

2003-09-27	Initial import of mummer, one of the many packages provided by	jschauma	5	-0/+137
	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.