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README.md 1.01 KiB

This is the description how to connect to the LabKey through API:

  1. Create a file named ".netrc" in your home directory. This file must include the following three lines:
    machine "remote-instance-of-labkey-server"
    login "user-email"
    password "user-password"

E.g.:

machine labkey.scicore.unibas.ch
login eva.pujadas@unibas.ch
password xxxxx

To secure the file, set permissions in a way that only you can see the content of the file:
$ chmod 400 .netrc

  1. For running the script labkey_api.py libraries "labkey" and "pandas" are required. Either you install them and run the script with the standard python or you use the module "labkey-api-python/1.1.0-foss-2018b-Python-3.6.6" provided by SciCore. Execute the following command:
    python labkey_api.py arg1 arg2
    Here, arg1 stands for the project name, arg2 stands for the name of the LabKey table.

E.g.:
python labkey_api.py TEST_ABOERSCH RNA_Seq_data_template

The script outputs the complete LabKey table in the form of pandas data frame.