recipe circtools

circtools - a circular RNA toolbox

Homepage:

https://github.com/jakobilab/circtools

Documentation:

https://docs.circ.tools/en/latest/

License:

GPL-3.0

Recipe:

/circtools/meta.yaml

Links:

doi: 10.1093/bioinformatics/bty948, biotools: circtools

package circtools

versions:

1.3.1-0,  1.3.0-0,  1.2.2-0,  1.2.1-0

depends bioconductor-ballgown:

depends bioconductor-biomart:

depends bioconductor-edger:

depends bioconductor-genomicfeatures:

depends bioconductor-genomicranges:

depends bioconductor-ggbio:

depends biopython:

>=1.71

depends htseq:

>=2.0.0

depends numpy:

>=1.14.5

depends pandas:

>=0.25.0

depends pathos:

>=0.3.0

depends pybedtools:

>=0.7.10

depends pysam:

>=0.16.0.1

depends python:

>=3.8

depends r-amap:

depends r-aod:

depends r-base:

depends r-data.table:

depends r-devtools:

depends r-dplyr:

depends r-formattable:

depends r-ggfortify:

depends r-ggplot2:

depends r-ggrepel:

depends r-gplots:

depends r-gridextra:

depends r-hmisc:

depends r-kableextra:

depends r-openxlsx:

depends r-plyr:

depends r-rcolorbrewer:

depends r-reshape2:

depends reportlab:

>=3.3.0

depends scipy:

>=0.19.0

depends star:

depends statsmodels:

depends stringtie:

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 circtools

and update with::

   mamba update circtools

To create a new environment, run:

mamba create --name myenvname circtools

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/circtools:<tag>

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

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