This (experimental) Docker image contains the latest versions of the following NCBI software:

• BLAST+ command line applications
• MagicBLAST
• EDirect
• SRA Toolkit

Please see the NCBI BLAST+ Docker image documentation and replace ncbi/blast with ncbi/workbench.

docker run --rm \ -v $HOME/queries:/blast/queries:rw \ ncbi/workbench \ sh -c 'efetch -db protein -id NP_002377 -format fasta > /blast/queries/NP_002377.fsa'

You can verify the results of this command on the local host as follows:

ls -l $HOME/queries

The test.sh script shows some additional sample commands.

docker run --rm -it ncbi/workbench fastq-dump --stdout SRR390728 | head -n 8

A Makefile is provided to conveniently maintain this docker image. It contains the variables USERNAME and VERSION which can be configured at runtime to faciliate maintenance, e.g.:

• make build VERSION=0.2: builds the docker image and tags it with version 0.2 and latest
• make publish USERNAME=ronaldo: publishes the image to Docker Hub under the name ronaldo/workbench
• make check: performs a sanity check on the most recently built image using default values (e.g.: ncbi/workbench)