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We just rebooted with several updates: * new HMTLify code * no port maintainer is now highly visible (e.g. https://freshports.org/security/sssd/) * fixed search logic error when using plain/ text details at https://github.com/FreshPorts/freshports/releases/tag/2.2.34
Port details
p5-transdecoder Identify candidate coding regions within transcript sequences
5.7.0 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: 2016-03-16 20:12:42
Last Update: 2023-01-30 22:30:54
Commit Hash: 8aad5af
Also Listed In: perl5
License: BSD3CLAUSE
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
Expand this list (48 items)
Collapse this list.
  1. /usr/local/share/licenses/p5-transdecoder-5.7.0/catalog.mk
  2. /usr/local/share/licenses/p5-transdecoder-5.7.0/LICENSE
  3. /usr/local/share/licenses/p5-transdecoder-5.7.0/BSD3CLAUSE
  4. bin/TransDecoder.LongOrfs
  5. bin/TransDecoder.Predict
  6. lib/perl5/site_perl/transdecoder/DelimParser.pm
  7. lib/perl5/site_perl/transdecoder/Fasta_reader.pm
  8. lib/perl5/site_perl/transdecoder/Fasta_retriever.pm
  9. lib/perl5/site_perl/transdecoder/GFF3_utils2.pm
  10. lib/perl5/site_perl/transdecoder/GTF.pm
  11. lib/perl5/site_perl/transdecoder/GTF_utils2.pm
  12. lib/perl5/site_perl/transdecoder/Gene_obj.pm
  13. lib/perl5/site_perl/transdecoder/Longest_orf.pm
  14. lib/perl5/site_perl/transdecoder/Nuc_translator.pm
  15. lib/perl5/site_perl/transdecoder/Overlap_piler.pm
  16. lib/perl5/site_perl/transdecoder/PWM.pm
  17. lib/perl5/site_perl/transdecoder/Pipeliner.pm
  18. lib/perl5/site_perl/transdecoder/Process_cmd.pm
  19. lib/perl5/site_perl/transdecoder/overlapping_nucs.ph
  20. libexec/transdecoder/cdna_alignment_orf_to_genome_orf.pl
  21. libexec/transdecoder/compute_base_probs.pl
  22. libexec/transdecoder/exclude_similar_proteins.pl
  23. libexec/transdecoder/fasta_prot_checker.pl
  24. libexec/transdecoder/ffindex_resume.pl
  25. libexec/transdecoder/gene_list_to_gff.pl
  26. libexec/transdecoder/get_FL_accs.pl
  27. libexec/transdecoder/get_longest_ORF_per_transcript.pl
  28. libexec/transdecoder/get_top_longest_fasta_entries.pl
  29. libexec/transdecoder/gff3_file_to_bed.pl
  30. libexec/transdecoder/gff3_file_to_proteins.pl
  31. libexec/transdecoder/gff3_gene_to_gtf_format.pl
  32. libexec/transdecoder/gtf_genome_to_cdna_fasta.pl
  33. libexec/transdecoder/gtf_to_alignment_gff3.pl
  34. libexec/transdecoder/gtf_to_bed.pl
  35. libexec/transdecoder/nr_ORFs_gff3.pl
  36. libexec/transdecoder/pfam_runner.pl
  37. libexec/transdecoder/refine_gff3_group_iso_strip_utrs.pl
  38. libexec/transdecoder/refine_hexamer_scores.pl
  39. libexec/transdecoder/remove_eclipsed_ORFs.pl
  40. libexec/transdecoder/score_CDS_likelihood_all_6_frames.pl
  41. libexec/transdecoder/select_best_ORFs_per_transcript.pl
  42. libexec/transdecoder/seq_n_baseprobs_to_loglikelihood_vals.pl
  43. libexec/transdecoder/start_codon_refinement.pl
  44. libexec/transdecoder/train_start_PWM.pl
  45. libexec/transdecoder/uri_unescape.pl
  46. @owner
  47. @group
  48. @mode
Collapse this list.
Dependency lines:
  • p5-transdecoder>0:biology/p5-transdecoder
To install the port:
cd /usr/ports/biology/p5-transdecoder/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/p5-transdecoder
  • pkg install p5-transdecoder
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: p5-transdecoder
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
p5-transdecoder
ABIlatestquarterly
FreeBSD:11:aarch642.1.0_15.4.0_2
FreeBSD:11:amd645.4.0_25.4.0_2
FreeBSD:11:armv62.1.05.4.0_2
FreeBSD:11:i3865.4.0_25.4.0_2
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips642.1.05.4.0_2
FreeBSD:12:aarch642.1.0_15.4.0_2
FreeBSD:12:amd645.7.05.4.0_2
FreeBSD:12:armv62.1.0_15.4.0_2
FreeBSD:12:armv72.1.0_15.4.0_2
FreeBSD:12:i3865.7.05.4.0_2
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips642.1.0_15.4.0_2
FreeBSD:12:powerpc64pkg-fallout5.4.0_2
FreeBSD:13:aarch645.7.05.4.0_2
FreeBSD:13:amd645.7.05.4.0_2
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv75.4.0_25.4.0_2
FreeBSD:13:i3865.7.05.4.0_2
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc645.4.0_25.4.0_2
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch645.4.0_2pkg-fallout
FreeBSD:14:amd645.7.0pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv75.4.0_2pkg-fallout
FreeBSD:14:i3865.7.0pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc645.4.0_2pkg-fallout
FreeBSD:14:riscv645.4.0_2pkg-fallout
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. cd-hit>=4.6.1 : biology/cd-hit
  2. p5-URI>0 : net/p5-URI
  3. perl5>=5.32.r0<5.33 : lang/perl5.32
There are no ports dependent upon this port

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/transdecoder/TransDecoder/tar.gz/TransDecoder-v5.7.0?dummy=/
Collapse this list.

Number of commits found: 13

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
5.7.0
30 Jan 2023 22:30:54
commit hash:8aad5af0deced3bf25bb2fad38bedf5865a81a05commit hash:8aad5af0deced3bf25bb2fad38bedf5865a81a05commit hash:8aad5af0deced3bf25bb2fad38bedf5865a81a05commit hash:8aad5af0deced3bf25bb2fad38bedf5865a81a05 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/p5-transdecoder: Update to 5.7.0

Numerous small fixes and enhancements since 5.4.0
Changes: https://github.com/TransDecoder/TransDecoder/tags

Reported by:    portscout
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)
5.4.0_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)
5.4.0_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
5.4.0_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.
5.4.0_2
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
5.4.0_1
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
5.4.0
23 Oct 2018 12:51:20
Revision:482836Original commit files touched by this commit
jwb search for other commits by this committer
biology/p5-transdecoder: Upgrade to 5.4.0

Minor clean up to silence portlint
Approved by:    jrm (mentor, implicit)
2.1.0_1
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).
2.1.0
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
2.1.0
03 Jan 2017 18:12:13
Revision:430490Original commit files touched by this commit
mat search for other commits by this committer
Never set WRKSRC when using USE_GITHUB.

If you want to set WRKSRC, set GH_PROJECT instead.
- The GitHub URLs are case insensitive, but the distribution files you
  get out of them are not.
- If the repository was renamed, the old URL will still work, but the
  distribution name will be ith the new name.

Sponsored by:	Absolight
2.1.0
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
2.1.0
16 Mar 2016 20:12:32
Revision:411246Original commit files touched by this commit
pi search for other commits by this committer
New port: biology/p5-transdecoder

TransDecoder identifies candidate coding regions within transcript
sequences, such as those generated by de novo RNA-Seq transcript
assembly using Trinity, or constructed based on RNA-Seq alignments
to the genome using Tophat and Cufflinks.

WWW: http://transdecoder.github.io/

PR:		207993
Submitted by:	Jason Bacon <bacon4000@gmail.com>

Number of commits found: 13