Package Recipe 'trinity'

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:

2.15.2-6, 2.15.2-5, 2.15.2-4, 2.15.2-3, 2.15.2-2, 2.15.2-1, 2.15.2-0, 2.15.1-4, 2.15.1-3,

2.15.2-6, 2.15.2-5, 2.15.2-4, 2.15.2-3, 2.15.2-2, 2.15.2-1, 2.15.2-0, 2.15.1-4, 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:

on _openmp_mutex >=4.5
on bioconductor-ctc
on bioconductor-dexseq
on bioconductor-edger
on bioconductor-go.db
on bioconductor-goseq
on bioconductor-qvalue
on bowtie2 >=2.3.0
on coreutils
on htslib >=1.22.1,<1.23.0a0
on kallisto
on kmer-jellyfish >=2.3
on libgcc >=13
on libgomp
on libstdcxx >=13
on libzlib >=1.3.1,<2.0a0
on numpy
on openjdk >=17
on perl >=5.32.1,<5.33.0a0 *_perl5
on perl-db_file
on python >=3.7
on r-ape
on r-argparse
on r-base
on r-cluster
on r-fastcluster
on r-gplots
on r-phangorn
on r-sm
on r-tidyverse
on r-vioplot
on salmon
on samtools >=1.14
on trimmomatic >=0.39

Additional platforms:

linux-aarch64, osx-arm64

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install trinity

to add into an existing workspace instead, run:

pixi add trinity

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install trinity

Alternatively, to install into a new environment, run:

conda create -n envname trinity

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/trinity/README.html)