Commit graph

6 commits

Author SHA1 Message Date
Joseph Mingrone
78fbf405d6 biology/cd-hit: Update to bug-fix release 4.6.6
Changes in version 4.6.6:
Bug fix for cd-hit-dup in variable length input when write out R1 reads

Changes in version 4.6.5:
Add filter for -aL option so that short sequences will be skipped if not
satisfy representative sequences' -aL requirement. This will make compute
faster in clustering settings where sequences in the same cluster are
required to have similar length using -aL -AL option (e.g. -aL 0.9).

Approved by:	AMDmi3 (mentor) swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8186
2016-12-20 16:48:12 +00:00
Mathieu Arnold
8b4093cba5 Do not use post-stage. Use post-install instead.
The only reason to use post-stage is because the port needs to do
"things" at a later time, like some plist manipulation.
While there, fold post-install in do-install targets when they are
defined.

PR:		214780
Submitted by:	mat
Exp-run by:	antoine
Sponsored by:	Absolight
2016-12-02 11:58:21 +00:00
Gerald Pfeifer
89f8b05214 Bump PORTREVISIONS for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

In particular that is ports with USE_GCC=yes, USE_GCC=any, or one of
gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang,
c++11-lang, c++0x, c11 requested via USES=compiler.
2016-11-20 09:38:08 +00:00
Martin Wilke
9146c80d02 - Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493
2015-12-11 08:48:56 +00:00
Wen Heping
4a34be3e77 - Use compiler:openmp instead of gcc
- Minor cleanup

Reported by:	danfe@
2015-09-19 13:12:44 +00:00
Wen Heping
cd1751b03f CD-HIT is a very widely used program for clustering and comparing protein or
nucleotide sequences.

WWW: http://weizhong-lab.ucsd.edu/cd-hit/

PR:		203183
Submitted by:	jwbacon@tds.net
2015-09-19 11:16:51 +00:00