recipe bioconductor-geofastq

Downloads ENA Fastqs With GEO Accessions






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

(downloads) docker_bioconductor-geofastq



depends r-base:


depends r-doparallel:

depends r-foreach:

depends r-plyr:

depends r-rcurl:

depends r-rvest:

depends r-stringr:

depends r-xml2:



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 bioconductor-geofastq

and update with::

   mamba update bioconductor-geofastq

To create a new environment, run:

mamba create --name myenvname bioconductor-geofastq

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 `bioconductor-geofastq/tags`_ for valid values for ``<tag>``)

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