recipe ncbi-vdb-py

SRA tools database engine (Python bindings)

Homepage:

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

License:

Public Domain

Recipe:

/ncbi-vdb-py/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. This package exposes the Python bindings and depends on ncbi-vdb to be available.

package ncbi-vdb-py

(downloads) docker_ncbi-vdb-py

versions:
3.1.1-0,  3.1.0-0,  3.0.10-0,  3.0.9-0,  3.0.8-0,  3.0.7-0,  3.0.6-0,  3.0.5-0,  3.0.2-0, 

3.1.1-0,  3.1.0-0,  3.0.10-0,  3.0.9-0,  3.0.8-0,  3.0.7-0,  3.0.6-0,  3.0.5-0,  3.0.2-0,  3.0.0-0,  2.11.0-0,  2.10.9-0,  2.10.8-0

depends ncbi-vdb:

3.1.1.*

depends python:

>=3.5

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 ncbi-vdb-py

and update with::

   mamba update ncbi-vdb-py

To create a new environment, run:

mamba create --name myenvname ncbi-vdb-py

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-py:<tag>

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

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Link to this page

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