ICGC tool for assisting EGA data submission


Keywords
ega, metadata, submission
License
GPL-3.0
Install
pip install egasub==0.1.0rc12

Documentation

Codacy Badge Build Status Coverage Status

EGASUB - ICGC EGA Submission CLI

EGASUB is a command line tool assists ICGC members submitting their NGS sequence data to EGA repository.

Installation

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"

Install latest egasub release

pipsi install egasub

Note: to install a specific version of egasub, e.g., 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 .

Run

Once installed, you can invoke the tool as follow. This will display information about how to use sub-commands and their options.

egasub

SOP for ICGC submitters

Detailed SOP for ICGC submitters is availabe here.

Support

Should you need assistance, please contact ICGC DCC at dcc-support@icgc.org.