- recipe trnanalysis
tRNA analysis pipeline
- Homepage:
- License:
MIT
- Recipe:
- package trnanalysis¶
- Versions:
0.1.10-1,0.1.10-0,0.1.9-0,0.1.8-1,0.1.8-0,0.1.7-2,0.1.7-1,0.1.7-0,0.1.6-1,0.1.10-1,0.1.10-0,0.1.9-0,0.1.8-1,0.1.8-0,0.1.7-2,0.1.7-1,0.1.7-0,0.1.6-1,0.1.6-0,0.1.5-0,0.1.4-0,0.1.2-0,0.1.0-0- Depends:
on bcftools
on bioconductor-deseq2
on bioconductor-org.hs.eg.db
on bowtie
on cgat-apps
on cgatcore
>=0.6.5on configparser
on ez_setup
on fastq-screen
on fastqc
on multiqc
on mysqlclient
on numpy
>=1.16.4on pandas
on pysam
0.15.2.*on python
>=3on pyyaml
>=5.1on r-base
on r-codetools
on r-dplyr
on r-dt
on r-fastqcr
on r-ggplot2
on r-ggpubr
on r-ggrepel
on r-ggthemes
on r-gridbase
on r-htmltools
on r-knitr
on r-optparse
on r-pheatmap
on r-plotly
on r-rcolorbrewer
on r-reshape2
on r-scales
on r-stringr
on r-tidyverse
on r-yaml
on ruffus
on samtools
on seaborn
on seqtk
on sortedcontainers
on subread
on trimmomatic
on trnascan-se
- Additional platforms:
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 trnanalysis
to add into an existing workspace instead, run:
pixi add trnanalysis
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 trnanalysis
Alternatively, to install into a new environment, run:
conda create -n envname trnanalysis
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/trnanalysis:<tag>
(see trnanalysis/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:
[](http://bioconda.github.io/recipes/trnanalysis/README.html)
