EGA python client - pyEGA3 pyEGA3 uses the EGA REST API to download authorized datasets and files Currently works only with Python3 REQUIREMENTS: Python "requests" module http://docs.python-requests.org/en/master/ pip3 install requests Firewall Ports This client makes https calls to the EGA AAI (https://ega.ebi.ac.uk:8443/) and to the EGA Data API (https://ega.ebi.ac.uk:8051). Both ports 8443 and 8051 must be reachable from the location where this client script is run. Otherwise you will experience timeouts. (e.g. https://ega.ebi.ac.uk:8443/ega-openid-connect-server/, https://ega.ebi.ac.uk:8051/elixir/central/stats/load should not time out). ------------------------------------------------------------------------- INSTALLATION via Pip: sudo pip3 install pyega3 ------------------------------------------------------------------------- INSTALLATION via Conda(Bioconda channel): conda config --add channels bioconda conda install pyega3 ------------------------------------------------------------------------- USAGE: pyega3 [-h] [-d] -cf CREDENTIALS_FILE [-c CONNECTIONS] {datasets,files,fetch} ... Download from EMBL EBI's EGA (European Genome-phenome Archive) positional arguments: {datasets,files,fetch} subcommands datasets List authorized datasets files List files in a specified dataset fetch Fetch a dataset or file optional arguments: -h, --help show this help message and exit -d, --debug Extra debugging messages -cf CREDENTIALS_FILE, --credentials-file CREDENTIALS_FILE JSON file containing credentials e.g.{'username':'user1','password':'toor'} -c CONNECTIONS, --connections CONNECTIONS Download using specified number of connections ------------------------------------------------------------------------- Credentials file supposed to be in json format e.g: { "username": "my.email@domain.edu", "password": "mypassword", "client_secret":"AMenuDLjVdVo4BSwi0QD54LL6NeVDEZRzEQUJ7hJOM3g4imDZBHHX0hNfKHPeQIGkskhtCmqAJtt_jm7EKq-rWw" } Your username and password are provided to you by EGA.