BSD Portsbiology/p5-transdecoder 6.0.0 FreeBSD
Identify candidate coding regions within transcript sequences
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- BSD3CLAUSE
- Categories
- biology, perl5
- Package size
- 90.7 KiB, 473.6 KiB installed
Description
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.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/p5-transdecoder | 6.0.0 |
| NetBSD | wip/p5-transdecoder | 5.3.0 |
| DragonFly | biology/p5-transdecoder | 5.7.1 |
| HardenedBSD | biology/p5-transdecoder | 6.0.0 |
| GhostBSD | biology/p5-transdecoder | 6.0.0 |
Install
Binary package:
pkg install p5-transdecoderFrom the ports tree:
cd /usr/ports/biology/p5-transdecoder/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= p5-transdecoder>0:biology/p5-transdecoderPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 6.0.0 | 6.0.0 | - | 5.7.1 | 6.0.0 |
| FreeBSD:14:quarterly | 6.0.0 | 6.0.0 | n/a | 5.7.1 | 6.0.0 |
| FreeBSD:15:latest | 6.0.0 | 6.0.0 | n/a | 5.7.1 | 5.7.1 |
| FreeBSD:15:quarterly | 6.0.0 | 6.0.0 | n/a | n/a | n/a |
| FreeBSD:16:latest | 6.0.0 | 6.0.0 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Runtime 2
cd-hit>=4.6.1: biology/cd-hitp5-URI>0: net/p5-URI
The full lists below include those, and their dependencies in turn.
Build dependencies 1
Run dependencies 5
No port depends on this one.
Configuration
No options to configure.
- USES
- perl5 shebangfix
- Service scripts
- none
Files
pkg-plist 43
- bin/TransDecoder
- bin/TransDecoder.LongOrfs
- bin/TransDecoder.Predict
- %%SITE_PERL%%/transdecoder/DelimParser.pm
- %%SITE_PERL%%/transdecoder/Fasta_reader.pm
- %%SITE_PERL%%/transdecoder/Fasta_retriever.pm
- %%SITE_PERL%%/transdecoder/GFF3_utils2.pm
- %%SITE_PERL%%/transdecoder/GTF.pm
- %%SITE_PERL%%/transdecoder/GTF_utils2.pm
- %%SITE_PERL%%/transdecoder/Gene_obj.pm
- %%SITE_PERL%%/transdecoder/Longest_orf.pm
- %%SITE_PERL%%/transdecoder/Nuc_translator.pm
- %%SITE_PERL%%/transdecoder/Overlap_piler.pm
- %%SITE_PERL%%/transdecoder/PWM.pm
- %%SITE_PERL%%/transdecoder/Pipeliner.pm
- %%SITE_PERL%%/transdecoder/Process_cmd.pm
- %%SITE_PERL%%/transdecoder/overlapping_nucs.ph
- libexec/transdecoder/cdna_alignment_orf_to_genome_orf.pl
- libexec/transdecoder/compute_base_probs.pl
- libexec/transdecoder/exclude_similar_proteins.pl
- libexec/transdecoder/fasta_prot_checker.pl
- libexec/transdecoder/ffindex_resume.pl
- libexec/transdecoder/gene_list_to_gff.pl
- libexec/transdecoder/get_FL_accs.pl
- libexec/transdecoder/get_longest_ORF_per_transcript.pl
- libexec/transdecoder/get_top_longest_fasta_entries.pl
- libexec/transdecoder/gff3_file_to_bed.pl
- libexec/transdecoder/gff3_file_to_proteins.pl
- libexec/transdecoder/gff3_gene_to_gtf_format.pl
- libexec/transdecoder/gtf_genome_to_cdna_fasta.pl
- libexec/transdecoder/gtf_to_alignment_gff3.pl
- libexec/transdecoder/gtf_to_bed.pl
- libexec/transdecoder/nr_ORFs_gff3.pl
- libexec/transdecoder/pfam_runner.pl
- libexec/transdecoder/refine_gff3_group_iso_strip_utrs.pl
- libexec/transdecoder/refine_hexamer_scores.pl
- libexec/transdecoder/remove_eclipsed_ORFs.pl
- libexec/transdecoder/score_CDS_likelihood_all_6_frames.pl
- libexec/transdecoder/select_best_ORFs_per_transcript.pl
- libexec/transdecoder/seq_n_baseprobs_to_loglikelihood_vals.pl
- libexec/transdecoder/start_codon_refinement.pl
- libexec/transdecoder/train_start_PWM.pl
- libexec/transdecoder/uri_unescape.pl
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| transdecoder-TransDecoder-TransDecoder-v6.0.0_GH0.tar.gz | 1.5755868e+07 | 53892ccedba4f8163adf4ffd0ceb2af1cf6685c6bae6f00491eeae74c3829799 |