Pynome, a Python command line interface tool, provides the user with a way to download desired genome assembly files from the Ensembl and NCBI databases.
Pip can be used for installation.
$ pip install .Commands can be run one at a time for crawling and mirroring.
Crawling:
$ pynome -cMirroring:
$ pynome -mOr strung together.
pynome -cmIndexing is designed to be done in parallel due to the large volume of assemblies that is mirrored. Parellel execution is done with two steps. The first step generated a list of pynome job files, each file being a single assembly whose indexes require updating. The second step is processing a single job and is meant to be done in parallel.
Generate job files:
pynome -IProcess a job file:
pynome -i -f <PATH>Where <PATH> is the path to a generated pynome job file that has the format 'pynome_job_#####.txt' where ##### is the job number.
The default root directory where assemblies are stored is $HOME/species. To change that to a different directory use the -d argument. For example to crawl using a custom directory:
$ pynome -d /custom -c