Python script for data downloads.

[spficklin]

Currently there are several scripts that get the data needed for AnnoTater. For the data sets that will use Diamond they must be indexed and currently the scripts have a Docker command hardcoded. That docker command does not work on HPC systems that only support Singularity nor on Kubernetes.

A solution to be more flexible would be to create a python script that could be more flexible.

The variables to consider providing to the script would be

1. The Annotater version: this would be used to specify the docker image names (e.g. annotater/diamond:0.9.25-[version])
2. The container manager: singularity or docker
3. Anything else that helps specify needed mount points (such as with Kubernetes).

[spficklin]

Here are the singularity command for Kamiak:

For the Uniprot SwissProt database. This command is meant to be run in the same directory as the data file. The -B ${PWD} argument mounts the current directory in the singularity image and singularity then runs diamond in the current working directory (same as mounted with -B)

singularity exec -B ${PWD} docker://annotater/diamond:0.9.25-0.9 diamond makedb --threads 4 --in uniprot_sprot.fasta 

[spficklin]

See PR #8