EGASUB - ICGC EGA Submission CLI
EGASUB is a command line tool assists ICGC members submitting their NGS sequence data to EGA repository.
Install pipsi first (if not installed yet)
# install pipsi curl https://raw.githubusercontent.com/mitsuhiko/pipsi/master/get-pipsi.py | python # modify PATH to find pipsi, you may want to add this to the '.bashrc' file export PATH="~/.local/bin:$PATH"
pipsi install egasub
Note: to install a specific version of
0.1.0rc11 do this:
pipsi install egasub==0.1.0rc11
Upgrade to latest release from an old one
pipsi upgrade egasub
If you'd like to play with the latest development version (not recommended for production use), install it from source as below.
# clone the source code git clone https://github.com/icgc-dcc/egasub.git # run tests cd egasub python setup.py test # install egasub pipsi install .
Once installed, you can invoke the tool as follow. This will display information about how to use sub-commands and their options.
SOP for ICGC submitters
Detailed SOP for ICGC submitters is availabe here.
Should you need assistance, please contact ICGC DCC at firstname.lastname@example.org.