pegi3s/ncbi-datasets repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image allows the usage of the NCBI Datasets⁠ resource to easily gather data from across NCBI databases.

It comes with two commands: datasets and dataformat. To obtain the help of them, you just need to run docker run --rm pegi3s/ncbi-datasets datasets --help or docker run --rm pegi3s/ncbi-datasets dataformat --help.

⁠Using the NCBI Datasets image in Linux

To use the applications, you should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/ncbi-datasets <command> <subcommand> <options>.

In this command, you should replace:

• /your/data/dir to point to the directory where you may store downloaded data.
• <command> the main command to use (datasets or dataformat).
• <subcommand> the name of the specific subcommand to use.
• <options> the specific command and subcommand options.

For instance, the following command will download the gene with GeneID 672 into gene_672.zip: docker run --rm -v /your/data/dir:/data pegi3s/ncbi-datasets datasets download gene gene-id 672 --filename /data/gene_672.zip

⁠Using the NCBI Datasets image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

As in the Linux case, to run an application, you should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/ncbi-datasets <command> <subcommand> <options>