Genome collection script for the SciDAS project.
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pynome
scripts
tests
.gitignore
.travis.yml
Dockerfile
README.md
docker-compose.yml
pynome_config.json
requirements.txt
setup.py

README.md

Pynome

Pynome, a Python command line interface tool, provides the user with a way to download desired genome assembly files from the Ensembl database.

Installation

$ python setup.py install

Usage

Commands can be run one at a time:

$ pynome discover
$ pynome list
$ pynome download
$ pynome prepare

Or strung together.

pynome discover download prepare

Docker Implementation

Pynome can be run as a Docker application. For iRODs integration you must create a docker secret named irods_password with the password of the iRODs user to be used to put files into iRODs.

The docker node used must be part of a swarm.

$ docker swarm init

TODO

  • Add delete() functions.