recipe sra-tools

SRA Toolkit and SDK from NCBI

Homepage:

https://github.com/ncbi/sra-tools

License:

Public Domain

Recipe:

/sra-tools/meta.yaml

The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.

package sra-tools

versions:

3.0.9-0,  3.0.8-0,  3.0.7-0,  3.0.6-0,  3.0.5-1,  3.0.5-0,  3.0.3-0,  3.0.0-1,  3.0.0-0, 

3.0.9-0,  3.0.8-0,  3.0.7-0,  3.0.6-0,  3.0.5-1,  3.0.5-0,  3.0.3-0,  3.0.0-1,  3.0.0-0,  2.11.0-3,  2.11.0-2,  2.11.0-1,  2.11.0-0,  2.10.9-0,  2.10.8-0,  2.10.7-2,  2.10.7-1,  2.10.7-0,  2.10.3-0,  2.10.1-0,  2.10.0-0,  2.9.6-0,  2.9.1_1-0,  2.9.1-0,  2.9.0-1,  2.8.2-1,  2.8.2-0,  2.8.1-0,  2.8.0-0,  2.7.0-0,  2.6.3-0,  2.6.2-0

depends ca-certificates:

depends curl:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends ncbi-vdb:

>=3.0.9

depends ossuuid:

depends perl:

depends perl-uri:

depends perl-xml-libxml:

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 sra-tools

and update with::

   mamba update sra-tools

To create a new environment, run:

mamba create --name myenvname sra-tools

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/sra-tools:<tag>

(see `sra-tools/tags`_ for valid values for ``<tag>``)

Notes

After installation, you should run the configuration tool: ./vdb-config -i. This tool will setup your download/cache area for downloaded files and references.

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