Package Recipe 'drop'

recipe drop

Detection of RNA Outlier Pipeline

Homepage:: https://github.com/gagneurlab/drop
Documentation:: https://gagneurlab-drop.readthedocs.io/en/latest/
License:: OTHER / MIT
Recipe:: /drop/meta.yaml
Links:: https: :https:`//doi.org/10.1038/s41596-020-00462-5`

package drop¶

Versions:

1.6.1-0, 1.6.0-0, 1.5.0-1, 1.5.0-0, 1.4.0-0, 1.3.4-0, 1.3.3-0, 1.3.2-0, 1.3.1-0,

1.6.1-0, 1.6.0-0, 1.5.0-1, 1.5.0-0, 1.4.0-0, 1.3.4-0, 1.3.3-0, 1.3.2-0, 1.3.1-0, 1.3.0-0, 1.2.4-0, 1.2.3-0, 1.2.2-0, 1.2.1-0, 1.1.4-0, 1.1.3-0, 1.1.2-0, 1.1.1-0, 1.1.0-0, 1.0.5-0, 1.0.4-0, 1.0.3-1, 1.0.3-0, 1.0.2-0, 1.0.1-0, 1.0.0-0, 0.9.2-0, 0.9.1-0, 0.9.0-0

Depends:

on bc
on bcftools >=1.9
on bioconductor-deseq2
on bioconductor-fraser >=2.6
on bioconductor-genomicscores
on bioconductor-outrider >=1.28
on bioconductor-variantannotation
on click >=7.0
on click-log
on gatk4 >=4.0.4
on graphviz
on htslib
on pandas >=3.0
on pandoc
on python >=3.11
on python-dateutil
on r-base >=4.0.0
on r-cowplot
on r-data.table
on r-devtools
on r-dplyr
on r-dt
on r-ggplot2
on r-ggthemes
on r-knitr
on r-magrittr
on r-rmarkdown
on r-tidyr
on r-tmae >=1.0.5
on samtools >=1.9
on snakemake-minimal >=5.5.2
on star >=2.7
on wbuild >=1.8 pyhdfd78af_2
on wget

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 drop

to add into an existing workspace instead, run:

pixi add drop

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 drop

Alternatively, to install into a new environment, run:

conda create -n envname drop

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/drop:<tag>

(see drop/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/drop/README.html)