CLI client for SP3

Python 3.6+

$ pip3 install -r requirements.txt

Copy config.json-example to config.json and edit it

Copy config.json-covid to config.json and edit it

You must edit at least username, password and sp3_url

The rest of the configuration relates to running the TB or Covid pipeline in an automated way.

Since this file contains your login details, please ensure that it is only readable by you.

$ python3 catsgo.py go <fetch_path>

e.g $ python3 catsgo.py go /data/inputs/system/sp3_test_data 

$ python3 catsgo.py download-report {run_uuid} {sample_name} > one_report.json

e.g. $ python3 catsgo.py download-report 87b3e6dc-9b6c-42f2-8574-0a1eab0f6c90 SRR7800670 > SRR7800670.json

$ python3 catsgo.py download-reports {pipeline_name} {run_uuid} > run_reports.json

e.g. $ python3 catsgo.py download-reports  oxforduni-Clockwork_combined 87b3e6dc-9b6c-42f2-8574-0a1eab0f6c90 > run_87b3e6dc.json

$ python3 report2csv.py run_reports.json > run_reports.csv

e.g. $ python3 report2csv.py run_87b3e6dc.json > run_87b3e6dc.csv

• Illumina pipeline

  $ python3 catsgo.py run-covid-illumina {pipeline_name} {data_path}

It is possible (but unlikely) that the sp3 server will clear your session between the login and the next request resulting in an unhandled failure.

Note that the report functions run after a run is finished. Therefore it is not guarateed that all reports will be finished just because a run is done. Some reports may take a long time to run. You should check if your required report type is present, and if not, re-queue your request.