:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'trnanalysis' .. highlight: bash trnanalysis =========== .. conda:recipe:: trnanalysis :replaces_section_title: :noindex: tRNA analysis pipeline :homepage: https://trnanalysis.readthedocs.io/en/latest/ :license: MIT :recipe: /`trnanalysis `_/`meta.yaml `_ .. conda:package:: trnanalysis |downloads_trnanalysis| |docker_trnanalysis| :versions: .. raw:: html
0.1.10-10.1.10-00.1.9-00.1.8-10.1.8-00.1.7-20.1.7-10.1.7-00.1.6-1 ``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`` .. raw:: html
:depends bcftools: :depends bioconductor-deseq2: :depends bioconductor-org.hs.eg.db: :depends bowtie: :depends cgat-apps: :depends cgatcore: ``>=0.6.5`` :depends configparser: :depends ez_setup: :depends fastq-screen: :depends fastqc: :depends multiqc: :depends mysqlclient: :depends numpy: ``>=1.16.4`` :depends pandas: :depends pysam: ``0.15.2.*`` :depends python: ``>=3`` :depends pyyaml: ``>=5.1`` :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: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`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 quay.io/biocontainers/trnanalysis: (see `trnanalysis/tags`_ for valid values for ````) .. |downloads_trnanalysis| image:: https://img.shields.io/conda/dn/bioconda/trnanalysis.svg?style=flat :target: https://anaconda.org/bioconda/trnanalysis :alt: (downloads) .. |docker_trnanalysis| image:: https://quay.io/repository/biocontainers/trnanalysis/status :target: https://quay.io/repository/biocontainers/trnanalysis .. _`trnanalysis/tags`: https://quay.io/repository/biocontainers/trnanalysis?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| 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/trnanalysis/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/trnanalysis/README.html