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, usegalaxy-eu: trinity, doi: 10.1038/nbt.1883, doi: 10.1038/nprot.2013.084

package trinity

versions:

2.15.1-3,  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, 

2.15.1-3,  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

depends bioconductor-ctc:

depends bioconductor-dexseq:

depends bioconductor-edger:

depends bioconductor-go.db:

depends bioconductor-goseq:

depends bioconductor-qvalue:

depends bowtie2:

>=2.3.0

depends htslib:

>=1.17,<1.19.0a0

depends kallisto:

depends kmer-jellyfish:

>=2.3

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends numpy:

depends openjdk:

>=17

depends perl:

>=5.32.1,<5.33.0a0 *_perl5

depends perl-db_file:

depends python:

>=3.7

depends r-ape:

depends r-argparse:

depends r-base:

depends r-cluster:

depends r-fastcluster:

depends r-gplots:

depends r-phangorn:

depends r-sm:

depends r-tidyverse:

depends r-vioplot:

depends salmon:

depends samtools:

>=1.14

depends trimmomatic:

>=0.39

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install trinity

and update with::

   mamba update trinity

To create a new environment, run:

mamba create --name myenvname trinity

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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