recipe iseq

iSeq is a Bash script that allows you to download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.

Homepage:

https://github.com/BioOmics/iSeq

License:

MIT / MIT

Recipe:

/iseq/meta.yaml

package iseq

(downloads) docker_iseq

versions:

1.2.0-1,  1.2.0-0,  1.1.0-0,  1.0.0-0

depends aspera-cli:

depends axel:

depends pigz:

depends sra-tools:

>=2.11.0

depends wget:

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 iseq

and update with::

   mamba update iseq

To create a new environment, run:

mamba create --name myenvname iseq

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/iseq:<tag>

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

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Link to this page

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