pkgsrc - [no description]

Age	Commit message (Collapse)	Author	Files	Lines
2015-11-02	Add SHA512 digests for distfiles for biology category.	agc	1	-1/+2
	Existing SHA1 digests verified, all found to be the same on the machine holding the existing distfiles (morden). Existing SHA1 digests retained for now as an audit trail.
2014-10-09	Remove pkgviews: don't set PKG_INSTALLATION_TYPES in Makefiles.	wiz	1	-3/+1

2012-09-11	"user-destdir" is default these days	asau	1	-2/+1

2010-09-19	Update lucy to 1.20.	obache	2	-8/+13
	Based on PR#43777 by Kamel Derouiche, with some clean up by me. Version 1.20, 9/3/2008. This version fixes a bug that caused lucy to fail when there was too much information on the FASTA header lines in the input files. Lucy had a 256 character buffer for reading lines from the input files. If any FASTA header lines were longer than 256 characters, the remaining characters would get read as part of the FASTA sequence. The solution implemented in this version is simply to increase the buffer size to 4096 characters. While that still leaves the potential for the same error to occur with extremely long header lines, the limitation that this entails seems reasonable, and this should fix the problem for all pratical purposes. --------------------------------------------------------------------- Version 1.19, 12/30/2003. This version fixes a bug that could cause sequences to be rejected incorrectly in the vector detection step (phase 6). Because of the way that lucy compares "tags" in the target sequence with "tags" in the vector sequence, some bases in the target sequence could get counted more than once in the tally of bases that match the vector sequence. In rare instances, this could cause the sequence to exceed the minimum threshold for rejection, as a result of random sequence similarity. The reporting of the CLB range in the -debug output file has also been changed. If the CLB range begins with the first base of the sequence, then the left coordinate of the CLB range will be reported as 1 (instead of 0). The range "CLB 0 0" still indicates an empty CLB range.
2009-06-14	Remove @dirrm entries from PLISTs	joerg	1	-2/+1

2009-06-12	Made the Makefile simpler.	rillig	2	-10/+7
	Removed unnecessary .gz suffix from man pages.
2009-05-16	update homepage, update master site.	zafer	1	-3/+3

2008-03-03	Mechanical changes to add full DESTDIR support to packages that install	jlam	1	-5/+7
	their files via a custom do-install target.
2007-01-07	Mechanically replaced man/* with ${PKGMANDIR}/* in the definition of	rillig	1	-3/+3
	INSTALLATION_DIRS, as well as all occurrences of ${PREFIX}/man with ${PREFIX}/${PKGMANDIR}. Fixes PR 35265, although I did not use the patch provided therein.
2006-10-04	Update MASTER_SITES and/or HOMEPAGE, from Sergey Svishchev.	wiz	1	-2/+2

2005-12-13	Don't hard-wire -lpthread, use PTHREAD_*.	joerg	2	-4/+4

2005-05-25	Add RMD160 checksum.	wiz	1	-1/+2

2005-03-26	Import lucy from pkgsrc-wip. Packaged by David Price and modified by me.	minskim	6	-0/+113
	A Sequence Cleanup Program. Lucy is a utility that prepares raw DNA sequence fragments for sequence assembly,possibly using the TIGR Assembler. The cleanup process includes quality assessment, confidence reassurance, vector trimming and vector removal. The primary advantage of Lucy over other similar utilities is that it is a fully integrated, stand alone program.