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Port details
cd-hit Clustering and comparing protein or nucleotide sequences
4.8.1_2 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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2015-09-19 11:17:00
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: GPLv2
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (43 items)
Collapse this list.
  1. /usr/local/share/licenses/cd-hit-4.8.1_2/catalog.mk
  2. /usr/local/share/licenses/cd-hit-4.8.1_2/LICENSE
  3. /usr/local/share/licenses/cd-hit-4.8.1_2/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. @owner
  42. @group
  43. @mode
Collapse this list.
Dependency lines:
  • cd-hit>0:biology/cd-hit
To install the port:
cd /usr/ports/biology/cd-hit/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/cd-hit
  • pkg install cd-hit
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: cd-hit
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
cd-hit
ABIlatestquarterly
FreeBSD:11:aarch644.6.6_44.8.1_1
FreeBSD:11:amd644.8.1_24.8.1_2
FreeBSD:11:armv64.6.44.8.1_1
FreeBSD:11:i3864.8.1_24.8.1_2
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips644.6.44.8.1_1
FreeBSD:12:aarch644.6.6_44.8.1_2
FreeBSD:12:amd644.8.1_24.8.1_2
FreeBSD:12:armv64.6.6_44.8.1_1
FreeBSD:12:armv74.6.6_44.8.1_1
FreeBSD:12:i3864.8.1_24.8.1_2
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips644.6.6_44.8.1_1
FreeBSD:12:powerpc64pkg-fallout4.8.1_2
FreeBSD:13:aarch644.8.1_24.8.1_2
FreeBSD:13:amd644.8.1_24.8.1_2
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv74.8.1_24.8.1_2
FreeBSD:13:i3864.8.1_24.8.1_2
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc644.8.1_14.8.1_2
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch644.8.1_2pkg-fallout
FreeBSD:14:amd644.8.1_2pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv74.8.1_2pkg-fallout
FreeBSD:14:i3864.8.1_2pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc644.8.1_2pkg-fallout
FreeBSD:14:riscv644.8.1_2pkg-fallout
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
This port is required by:
for Run
  1. biology/biostar-tools
  2. biology/ddocent
  3. biology/p5-transdecoder

Configuration Options:
Options name:
USES:
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/weizhongli/cdhit/tar.gz/V4.8.1?dummy=/
Collapse this list.

Number of commits found: 22

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
4.8.1_2
07 Sep 2022 21:10:59
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
4.8.1_2
27 Apr 2022 13:22:07
commit hash:74016ad026a87ddbf04a85e76c9bdb2ecbbffcf5commit hash:74016ad026a87ddbf04a85e76c9bdb2ecbbffcf5commit hash:74016ad026a87ddbf04a85e76c9bdb2ecbbffcf5commit hash:74016ad026a87ddbf04a85e76c9bdb2ecbbffcf5 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/cd-hit: check for omp.h on all architectures
4.8.1_2
21 Nov 2021 13:26:44
commit hash:6b73ac038575fd8031219a1a554483087a8940c2commit hash:6b73ac038575fd8031219a1a554483087a8940c2commit hash:6b73ac038575fd8031219a1a554483087a8940c2commit hash:6b73ac038575fd8031219a1a554483087a8940c2 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/cd-hit: fix build on armv7

Same issue as on powerpc.
4.8.1_2
10 Jun 2021 00:35:36
commit hash:8aae744d04920573ee2c3c34390c268a05beff39commit hash:8aae744d04920573ee2c3c34390c268a05beff39commit hash:8aae744d04920573ee2c3c34390c268a05beff39commit hash:8aae744d04920573ee2c3c34390c268a05beff39 files touched by this commit
Piotr Kubaj (pkubaj) search for other commits by this committer
biology/cd-hit: fix build on powerpc

LLVM on powerpc doesn't have libomp:
cdhit-common.c++:36:9: fatal error: 'omp.h' file not found
4.8.1_2
07 Apr 2021 08:09:01
commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
4.8.1_2
06 Apr 2021 14:31:07
commit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
4.8.1_2
11 Jan 2021 16:55:15
Revision:561228Original commit files touched by this commit
jwb search for other commits by this committer
biology/cd-hit: Drop dependency on gcc

Simply remove compiler:openmp
Builds with base compiler on amd64, i386, and powerpc64

PR:             port/247753, ports/252379
4.8.1_1
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

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, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
4.8.1
14 Mar 2019 23:59:48
Revision:495746Original commit files touched by this commit
jwb search for other commits by this committer
biology/cd-hit: Upgrade to 4.8.1

Convert Makefile REINPLACE to patch for sending upstream
4.6.6_5
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
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
4.6.6_4
29 Jul 2018 22:18:46
Revision:475857Original commit files touched by this commit
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
4.6.6_3
10 Mar 2018 17:46:06
Revision:464084Original commit files touched by this commit
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).
4.6.6_2
31 Jan 2018 01:07:08
Revision:460452Original commit files touched by this commit
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
4.6.6_2
10 Sep 2017 20:55:39
Revision:449591Original commit files touched by this commit
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
4.6.6_1
01 Apr 2017 15:23:32
Revision:437439Original commit files touched by this commit
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
4.6.6
20 Dec 2016 16:48:12
Revision:429002Original commit files touched by this commit
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
4.6.4_1
02 Dec 2016 11:58:22
Revision:427552Original commit files touched by this commit
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
4.6.4_1
20 Nov 2016 09:38:09
Revision:426566Original commit files touched by this commit
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.
4.6.4
11 Dec 2015 08:48:57
Revision:403506Original commit files touched by this commit
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
4.6.4
19 Sep 2015 13:12:44
Revision:397322Original commit files touched by this commit
wen search for other commits by this committer
- Use compiler:openmp instead of gcc
- Minor cleanup

Reported by:	danfe@
4.6.4
19 Sep 2015 11:16:52
Revision:397318Original commit files touched by this commit
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: 22