Package Recipe 'bioconductor-geofastq'

recipe bioconductor-geofastq

Downloads ENA Fastqs With GEO Accessions

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/GEOfastq.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-geofastq/meta.yaml

GEOfastq is used to download fastq files from the European Nucleotide Archive (ENA) starting with an accession from the Gene Expression Omnibus (GEO). To do this, sample metadata is retrieved from GEO and the Sequence Read Archive (SRA). SRA run accessions are then used to construct FTP and aspera download links for fastq files generated by the ENA.

package bioconductor-geofastq¶

Versions:

1.18.0-0, 1.14.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-0, 1.2.0-0, 1.0.0-0

Depends:

on r-base >=4.5,<4.6.0a0
on r-doparallel
on r-foreach
on r-plyr
on r-rcurl
on r-rvest
on r-stringr
on r-xml2

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 bioconductor-geofastq

to add into an existing workspace instead, run:

pixi add bioconductor-geofastq

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 bioconductor-geofastq

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-geofastq

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/bioconductor-geofastq:<tag>

(see bioconductor-geofastq/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/bioconductor-geofastq/README.html)