recipe trinity

Trinity assembles transcript sequences from Illumina RNA-Seq data.

Homepage:

https://github.com/trinityrnaseq/trinityrnaseq/

Documentation:

https://github.com/trinityrnaseq/trinityrnaseq/wiki

License:

BSD / BSD-3-Clause

Recipe:

/trinity/meta.yaml

Links:

biotools: trinity, doi: 10.1038/nbt.1883, usegalaxy-eu: trinity

package trinity

Versions:

2.15.1-2,  2.15.1-1,  2.15.1-0,  2.13.2-4,  2.13.2-3,  2.13.2-2,  2.13.2-1,  2.13.2-0,  2.12.0-3, 

2.15.1-2,  2.15.1-1,  2.15.1-0,  2.13.2-4,  2.13.2-3,  2.13.2-2,  2.13.2-1,  2.13.2-0,  2.12.0-3,  2.12.0-2,  2.12.0-1,  2.12.0-0,  2.11.0-1,  2.11.0-0,  2.9.1-1,  2.9.1-0,  2.8.5-5,  2.8.5-4,  2.8.5-3,  2.8.5-2,  2.8.5-1,  2.8.5-0,  2.8.4-1,  2.8.4-0,  2.8.3-0,  2.8.2-2,  2.8.2-1,  2.8.2-0,  2.6.6-2,  2.6.6-1,  2.6.6-0,  2.5.1-1,  2.5.1-0,  2.4.0-5,  2.4.0-4,  2.4.0-3,  2.3.2-2,  2.3.2-1,  2.3.2-0,  2.2.0-7,  2.2.0-6,  2.2.0-5,  2.2.0-4,  2.2.0-3,  2.2.0-2,  2.2.0-1,  2.2.0-0,  2.1.1-6,  date.2011_11_26-8,  date.2011_11_26-7,  date.2011_11_26-6,  date.2011_11_26-5,  date.2011_11_26-4,  date.2011_11_26-3

Depends:

• _openmp_mutex >=4.5

• bioconductor-ctc

• bioconductor-dexseq

• bioconductor-edger

• bioconductor-go.db

• bioconductor-goseq

• bioconductor-qvalue

• bowtie

• bowtie2 >=2.3.0

• coreutils

• htslib >=1.17,<1.18.0a0

• kallisto

• kmer-jellyfish >=2.2

• libgcc-ng >=12

• libstdcxx-ng >=12

• libzlib >=1.2.13,<1.3.0a0

• numpy

• openjdk >=8

• perl

• perl-db_file

• python >=3.6

• r-ape

• r-argparse

• r-base >=4.1

• r-cluster

• r-fastcluster

• r-gplots

• r-phangorn

• r-sm

• r-tidyverse

• r-vioplot

• salmon >=1.0

• samtools >=1.9

• trimmomatic >=0.36

Required By:

• guessmylt

• star-fusion

• discasm

• mitgard

• fusion-inspector

• funannotate

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install trinity

and update with:

conda update trinity

or use the docker container:

docker pull quay.io/biocontainers/trinity:<tag>

(see trinity/tags for valid values for <tag>)

Download stats

Link to this page

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