recipe genome_updater

genome_updater: bash script to download/update snapshots of refseq/genbank



MIT / MIT License



Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

package genome_updater

(downloads) docker_genome_updater



depends bc:

depends coreutils:

depends curl:

depends findutils:

depends gawk:

depends parallel:

depends tar:

depends wget:



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 genome_updater

and update with::

   mamba update genome_updater

To create a new environment, run:

mamba create --name myenvname genome_updater

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 `genome_updater/tags`_ for valid values for ``<tag>``)

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