recipe ncbi-vdb

SRA tools database engine.

Homepage:

https://github.com/ncbi/ncbi-vdb

Documentation:

https://github.com/ncbi/ncbi-vdb/wiki

License:

Public Domain

Recipe:

/ncbi-vdb/meta.yaml

"VDB is the database engine that all SRA tools use. It is a columnar database system with a number of unique features. All SRA objects are stored in VDB."

package ncbi-vdb

(downloads) docker_ncbi-vdb

versions:
3.2.1-0,  3.2.0-0,  3.1.1-3,  3.1.1-2,  3.1.1-1,  3.1.1-0,  3.1.0-2,  3.1.0-1,  3.1.0-0, 

3.2.1-0,  3.2.0-0,  3.1.1-3,  3.1.1-2,  3.1.1-1,  3.1.1-0,  3.1.0-2,  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,  3.0.5-2,  3.0.5-0,  3.0.2-2,  3.0.2-1,  3.0.2-0,  3.0.0-0,  2.11.0-1,  2.11.0-0,  2.10.9-0,  2.10.8-0,  2.10.7-0,  2.10.6-0,  2.10.5-0,  2.10.4-0,  2.10.3-0,  2.10.2-0,  2.10.1-0,  2.10.0-0,  2.9.6-0,  2.9.3-0,  2.9.1-0,  2.9.0-0

depends libgcc:

>=13

depends libstdcxx:

>=13

requirements:

additional platforms:
linux-aarch64,  osx-arm64

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 ncbi-vdb

and update with::

   mamba update ncbi-vdb

To create a new environment, run:

mamba create --name myenvname ncbi-vdb

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/ncbi-vdb:<tag>

(see `ncbi-vdb/tags`_ for valid values for ``<tag>``)

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