Open spficklin opened 4 years ago
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
See PR #8
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