From 22eea1b864ae7485d7f4c8366ca512e6950f4c30 Mon Sep 17 00:00:00 2001
From: Alex Kanitz <alexander.kanitz@unibas.ch>
Date: Fri, 24 Jan 2020 15:14:48 +0100
Subject: [PATCH] Update README.md
---
scripts/README.md | 57 ++++++++++++++++++++++++++++++-----------------
1 file changed, 36 insertions(+), 21 deletions(-)
diff --git a/scripts/README.md b/scripts/README.md
index 15d3dbb..389c8b7 100644
--- a/scripts/README.md
+++ b/scripts/README.md
@@ -1,23 +1,38 @@
-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
-
-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.:
+In order to connect to the LabKey through API, you will first need to create a file `.netrc` in your home directory:
+
+```bash
+touch ${HOME}/.netrc
+
+Add the following lines to the file:
+
+```console
+machine <remote-instance-of-labkey-server>
+login <user-email>
+password <user-password>
+```
+
+To secure the file, set permissions in a way that only you can see the content of the file:
+
+```bash
+chmod 400 .netrc
+```
+
+Install the `labkey` and `pandas` packages, ideally from a virtual environment (e.g., `virtualenv` or `conda`):
+
+```bash
+pip install labkey pandas
+```
+
+Run the LabKey API client script:
+
+```bash
+python labkey_api.py project_name labkey_table_nane
+```
+
+Example:
+
+```bash
python labkey_api.py TEST_ABOERSCH RNA_Seq_data_template
+```
-The script outputs the complete LabKey table in the form of pandas data frame.
+The script outputs the requested LabKey table in the form of a pandas data frame.
--
GitLab