Package Recipe 'sra-tools'

recipe sra-tools

The SRA Toolkit and SDK from NCBI.

Homepage:: https://github.com/ncbi/sra-tools
Documentation:: https://github.com/ncbi/sra-tools/wiki
License:: Public Domain
Recipe:: /sra-tools/meta.yaml
Links:: biotools: sra-tools

"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:

3.2.1-1, 3.2.1-0, 3.2.0-0, 3.1.1-2, 3.1.1-0, 3.1.0-1, 3.1.0-0, 3.0.10-0, 3.0.9-0,

3.2.1-1, 3.2.1-0, 3.2.0-0, 3.1.1-2, 3.1.1-0, 3.1.0-1, 3.1.0-0, 3.0.10-0, 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:

on ca-certificates
on curl
on libgcc
on libgcc-ng >=12
on libstdcxx
on libstdcxx-ng >=12
on ncbi-vdb >=3.2.1
on ncbi-vdb >=3.2.1,<4.0a0
on ossuuid
on perl
on perl-uri
on perl-xml-libxml

Additional platforms:

linux-aarch64, osx-arm64

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 sra-tools

to add into an existing workspace instead, run:

pixi add sra-tools

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 sra-tools

Alternatively, to install into a new environment, run:

conda create -n envname sra-tools

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/sra-tools:<tag>

(see sra-tools/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.

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.

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/sra-tools/README.html)