recipe trnanalysis

tRNA analysis pipeline






package trnanalysis

(downloads) docker_trnanalysis



depends bcftools:

depends bioconductor-deseq2:


depends bowtie:

depends cgat-apps:

depends cgatcore:


depends configparser:

depends ez_setup:

depends fastq-screen:

depends fastqc:

depends multiqc:

depends mysqlclient:

depends numpy:


depends pandas:

depends pysam:


depends python:


depends pyyaml:


depends r-base:

depends r-codetools:

depends r-dplyr:

depends r-dt:

depends r-fastqcr:

depends r-ggplot2:

depends r-ggpubr:

depends r-ggrepel:

depends r-ggthemes:

depends r-gridbase:

depends r-htmltools:

depends r-knitr:

depends r-optparse:

depends r-pheatmap:

depends r-plotly:

depends r-rcolorbrewer:

depends r-reshape2:

depends r-scales:

depends r-stringr:

depends r-tidyverse:

depends r-yaml:

depends ruffus:

depends samtools:

depends seaborn:

depends seqtk:

depends sortedcontainers:

depends subread:

depends trimmomatic:

depends trnascan-se:



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 trnanalysis

and update with::

   mamba update trnanalysis

To create a new environment, run:

mamba create --name myenvname trnanalysis

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<tag>

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

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