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Port details
cd-hit Clustering and comparing protein or nucleotide sequences
4.8.1 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-09-19 11:17:00
Last Update: 2019-03-14 23:59:48
SVN Revision: 495746
License: GPLv2
CD-HIT is a very widely used program for clustering and comparing protein or
nucleotide sequences.

WWW: http://weizhong-lab.ucsd.edu/cd-hit/
SVNWeb : Homepage : PortsMon
    Pseudo-pkg-plist information, but much better, from make generate-plist
    Expand this list (40 items)
  1. /usr/local/share/licenses/cd-hit-4.8.1/catalog.mk
  2. /usr/local/share/licenses/cd-hit-4.8.1/LICENSE
  3. /usr/local/share/licenses/cd-hit-4.8.1/GPLv2
  4. bin/FET.pl
  5. bin/cd-hit
  6. bin/cd-hit-2d
  7. bin/cd-hit-2d-para.pl
  8. bin/cd-hit-454
  9. bin/cd-hit-clstr_2_blm8.pl
  10. bin/cd-hit-div
  11. bin/cd-hit-div.pl
  12. bin/cd-hit-est
  13. bin/cd-hit-est-2d
  14. bin/cd-hit-para.pl
  15. bin/clstr2tree.pl
  16. bin/clstr2txt.pl
  17. bin/clstr2xml.pl
  18. bin/clstr_cut.pl
  19. bin/clstr_list.pl
  20. bin/clstr_list_sort.pl
  21. bin/clstr_merge.pl
  22. bin/clstr_merge_noorder.pl
  23. bin/clstr_quality_eval.pl
  24. bin/clstr_quality_eval_by_link.pl
  25. bin/clstr_reduce.pl
  26. bin/clstr_renumber.pl
  27. bin/clstr_rep.pl
  28. bin/clstr_reps_faa_rev.pl
  29. bin/clstr_rev.pl
  30. bin/clstr_select.pl
  31. bin/clstr_select_rep.pl
  32. bin/clstr_size_histogram.pl
  33. bin/clstr_size_stat.pl
  34. bin/clstr_sort_by.pl
  35. bin/clstr_sort_prot_by.pl
  36. bin/clstr_sql_tbl.pl
  37. bin/clstr_sql_tbl_sort.pl
  38. bin/make_multi_seq.pl
  39. bin/plot_2d.pl
  40. bin/plot_len1.pl
  41. Collapse this list.

Dependency line: cd-hit>0:biology/cd-hit


To install the port: cd /usr/ports/biology/cd-hit/ && make install clean
To add the package: pkg install cd-hit

PKGNAME: cd-hit

There is no flavor information for this port.

distinfo:

TIMESTAMP = 1552053543
SHA256 (weizhongli-cdhit-V4.8.1_GH0.tar.gz) = f8bc3cdd7aebb432fcd35eed0093e7a6413f1e36bbd2a837ebc06e57cdb20b70
SIZE (weizhongli-cdhit-V4.8.1_GH0.tar.gz) = 945639


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. gmake : devel/gmake

This port is required by:

for Run * - deleted ports are only shown under the This port is required by section. It was harder to do for the Required section. Perhaps later...
Configuration Options
     No options to configure

USES:
compiler:openmp gmake shebangfix

Master Sites:
  1. https://codeload.github.com/weizhongli/cdhit/tar.gz/V4.8.1?dummy=/

Number of commits found: 13

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
14 Mar 2019 23:59:48
Original commit files touched by this commit  4.8.1
Revision:495746
jwb search for other commits by this committer
biology/cd-hit: Upgrade to 4.8.1

Convert Makefile REINPLACE to patch for sending upstream
12 Dec 2018 01:35:36
Original commit files touched by this commit  4.6.6_5
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
29 Jul 2018 22:18:46
Original commit files touched by this commit  4.6.6_4
Revision:475857
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
10 Mar 2018 17:46:06
Original commit files touched by this commit  4.6.6_3
Revision:464084
gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
31 Jan 2018 01:07:08
Original commit files touched by this commit  4.6.6_2
Revision:460452
jwb search for other commits by this committer
Multiple ports:
Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org
Remove Created by comments for same user

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14128
10 Sep 2017 20:55:39
Original commit files touched by this commit  4.6.6_2
Revision:449591
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
(via Mk/bsd.default-versions.mk and lang/gcc) which has moved from
GCC 5.4 to GCC 6.4 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang,
   c++14-lang, c++0x, c11, or gcc-c++11-lib.

PR:		219275
01 Apr 2017 15:23:32
Original commit files touched by this commit  4.6.6_1
Revision:437439
gerald search for other commits by this committer
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using using Mk/bsd.octave.mk which in turn has USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
   c++11-lang, c++0x, c11, or gcc-c++11-lib.

PR:		216707
20 Dec 2016 16:48:12
Original commit files touched by this commit  4.6.6
Revision:429002
jrm search for other commits by this committer
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
02 Dec 2016 11:58:22
Original commit files touched by this commit  4.6.4_1
Revision:427552
mat search for other commits by this committer
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
20 Nov 2016 09:38:09
Original commit files touched by this commit  4.6.4_1
Revision:426566
gerald search for other commits by this committer
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.
11 Dec 2015 08:48:57
Original commit files touched by this commit  4.6.4
Revision:403506
miwi search for other commits by this committer
- Update maintainer mail address
- Update/Remove MASTER_SITE

PR:		204755
Submitted by:	 jwbacon@tds.net (maintainer)
Approved by:	mat (mentor)
Differential Revision:	D4493
19 Sep 2015 13:12:44
Original commit files touched by this commit  4.6.4
Revision:397322
wen search for other commits by this committer
- Use compiler:openmp instead of gcc
- Minor cleanup

Reported by:	danfe@
19 Sep 2015 11:16:52
Original commit files touched by this commit  4.6.4
Revision:397318
wen search for other commits by this committer
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

Number of commits found: 13

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