diff --git a/scripts/labkey_api.md b/scripts/labkey_api.md index 04e3ec02c00043d6249e48860319a84d6373cee1..5846e033aa7c989072064de7278df7e2202607c1 100644 --- a/scripts/labkey_api.md +++ b/scripts/labkey_api.md @@ -1,7 +1,9 @@ -> **NOTE**: Include this info in the main doc in the root directory once available +> **NOTE**: Include this info in the main doc in the root directory once +> available; add information on how to get credentials for the LabKey server +> (i.e., how to obatain a password for the `.netrc` file) -In order to connect to the LabKey through API, you will first need to create a file `.netrc` in your -home directory: +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 @@ -15,13 +17,15 @@ 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: +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`): +Install the `labkey` and `pandas` packages, ideally from a virtual environment +(e.g., `virtualenv` or `conda`): ```bash pip install labkey pandas @@ -39,5 +43,7 @@ Example: python labkey_api.py TEST_ABOERSCH RNA_Seq_data_template ``` -Right now the script prints a representation of a `pandas` data frame containing the requested LabKey table the the screen. -For further processing the current script could be included in another script, or it could be modified to write out the data in a desired file format (e.g., TSV). +Right now the script prints a representation of a `pandas` data frame +containing the requested LabKey table the the screen. For further processing +the current script could be included in another script, or it could be modified +to write out the data in a desired file format (e.g., TSV).