recipe bioconductor-sradb

A compilation of metadata from NCBI SRA and tools

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/SRAdb.html

License:

Artistic-2.0

Recipe:

/bioconductor-sradb/meta.yaml

Links:

biotools: sradb

The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.

package bioconductor-sradb

(downloads) docker_bioconductor-sradb

versions:
1.64.0-0,  1.62.0-0,  1.60.0-0,  1.56.0-0,  1.54.0-0,  1.52.0-1,  1.52.0-0,  1.50.0-0,  1.48.0-0, 

1.64.0-0,  1.62.0-0,  1.60.0-0,  1.56.0-0,  1.54.0-0,  1.52.0-1,  1.52.0-0,  1.50.0-0,  1.48.0-0,  1.46.0-1,  1.44.0-1,  1.44.0-0,  1.42.2-0,  1.37.0-0,  1.36.0-0,  1.32.0-0,  1.28.0-0

depends bioconductor-geoquery:

>=2.70.0,<2.71.0

depends bioconductor-graph:

>=1.80.0,<1.81.0

depends r-base:

>=4.3,<4.4.0a0

depends r-rcurl:

depends r-rsqlite:

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 bioconductor-sradb

and update with::

   mamba update bioconductor-sradb

To create a new environment, run:

mamba create --name myenvname bioconductor-sradb

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/bioconductor-sradb:<tag>

(see `bioconductor-sradb/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

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