From e544cc9321c3195d2e6013827268884c52ad3a5d Mon Sep 17 00:00:00 2001 From: "anastasiya.boersch@unibas.ch" <anastasiya.boersch@unibas.ch> Date: Fri, 24 Jan 2020 14:12:24 +0100 Subject: [PATCH] Update README --- scripts/README.md | 36 ++++++++++++++++++------------------ 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/scripts/README.md b/scripts/README.md index 5c32ea2..764586c 100644 --- a/scripts/README.md +++ b/scripts/README.md @@ -1,23 +1,23 @@ 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> +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 -E.g.: +To secure the file, set permissions in a way that only you can see the content of the file: +$ chmod 400 .netrc -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 - -2. 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 +2. 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. -- GitLab