recipe sracat

a command-line tool for extracting unordered read data from SRA files

Homepage:

https://github.com/lanl/sracat

License:

BSD / BSD-3-Clause

Recipe:

/sracat/meta.yaml

sracat is small C++ program that uses the NCBI sra-toolkit C++ API to extract sequence (and optionally quailty scores) from SRA records. Unlike the fasterq-dump program included with the sra-toolkit, sracat does not output the reads in their origianlly submitted order, but rather outputs reads in the order in which they are stored in the SRA file.

package sracat

(downloads) docker_sracat

versions:

0.2-2,  0.2-1,  0.2-0

depends ca-certificates:

depends libgcc-ng:

>=12

depends libstdcxx-ng:

>=12

depends libzlib:

>=1.2.13,<1.3.0a0

depends zlib:

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 sracat

and update with::

   mamba update sracat

To create a new environment, run:

mamba create --name myenvname sracat

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/sracat:<tag>

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

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