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Port details
p5-transdecoder Identify candidate coding regions within transcript sequences
5.4.0_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 5.4.0_2Version 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: 2021-04-07 08:09:01
Commit Hash: cf118cc
Also Listed In: perl5
License: BSD3CLAUSE
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (48 items)
Collapse this list.
  1. /usr/local/share/licenses/p5-transdecoder-5.4.0_2/catalog.mk
  2. /usr/local/share/licenses/p5-transdecoder-5.4.0_2/LICENSE
  3. /usr/local/share/licenses/p5-transdecoder-5.4.0_2/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
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:mips--
FreeBSD:11:mips642.1.05.4.0_2
FreeBSD:12:aarch642.1.0_15.4.0_2
FreeBSD:12:amd645.4.0_25.4.0_2
FreeBSD:12:armv62.1.0_15.4.0_2
FreeBSD:12:armv72.1.0_15.4.0_2
FreeBSD:12:i3865.4.0_25.4.0_2
FreeBSD:12:mips--
FreeBSD:12:mips642.1.0_15.4.0_2
FreeBSD:12:powerpc64-5.4.0_2
FreeBSD:13:aarch645.4.0_25.4.0_2
FreeBSD:13:amd645.4.0_25.4.0_2
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3865.4.0_25.4.0_2
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc645.4.0_25.4.0_2
FreeBSD:14:aarch645.4.0_2-
FreeBSD:14:amd645.4.0_2-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3865.4.0_2-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc645.4.0_2-
 

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-v5.4.0?dummy=/
Collapse this list.

Number of commits found: 10

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  5.4.0_2
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  5.4.0_2
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
26 Jul 2019 20:46:57
Original commit files touched by this commit Revision:507372  5.4.0_2
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
12 Dec 2018 01:35:36
Original commit files touched by this commit Revision:487272  5.4.0_1
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
23 Oct 2018 12:51:20
Original commit files touched by this commit Revision:482836  5.4.0
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)
10 Mar 2018 17:46:06
Original commit files touched by this commit Revision:464084  2.1.0_1
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 Revision:460452  2.1.0
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
03 Jan 2017 18:12:13
Original commit files touched by this commit Revision:430490  2.1.0
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
01 Apr 2016 13:29:17
Original commit files touched by this commit Revision:412344  2.1.0
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
16 Mar 2016 20:12:32
Original commit files touched by this commit Revision:411246  2.1.0
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: 10