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:

3.0.5-1,  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, 

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

• curl

• libgcc-ng >=12

• libstdcxx-ng >=12

• ncbi-vdb >=3.0.5

• ossuuid

• perl

• perl-uri

• perl-xml-libxml

Required By:

• minute

• kingfisher

• haphpipe

• bactopia-gather

• harvest-variants

• metapi

• mothur

• atlas-fastq-provider

• bioconvert

• riboraptor

• fusioncatcher

• uscdc-datasets-sars-cov-2

• biolite

• mashpit

• seqsero2

• parallel-fastq-dump

• fastq-dl

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install sra-tools

and update with:

conda update sra-tools

or 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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