PEGR Galaxy workflow - seqcode/pegr GitHub Wiki

1- Create a workflow in Galaxy with the name in the format of "Name_Version". Name should not have underscore or dashes. Version should be in the format of 001, 002 and so one. For example: "paired_002"

2- Introduce workflow to pegr in Admin->Pipeline->New Pipeline with the following information: Workflow Id : The number right at the end of the url of the workflow in Galaxy. url of the workflow in Galaxy can be found by click WorkFlow tab on the top panel of Galaxy -> click on the name of the desired workflow-> on the drop down menu click on view

Name : Name of the WorkFlow

Steps: [[“tool_1_id available in Galaxy XML wrapper”, “name_you_like_to_be_shown_in_PEGR_for_tool_1” ], [“tool_id of tool 2 available in Galaxy XML wrapper”, “name_you_like_to_be_shown_in_PEGR_for_tool_2”],….]

Workflow Url : Galaxy Website ->workflow Tab->right click on workflow-> view -> copy the url

Pipeline Version: For example 001

3- Create a user in PEGR with an email which should be similar to Email logged in Galaxy to run the pipeline.

4- Extract the API of the user in PEGR and give it as input to config file of pegr-galaxy communication file. PEGR URL should also be given with the following example format:

PEGR_API_KEY = my_pegr_api_key

PEGR_URL = https://myhostname/pegr/api/stats

**The API key will and PEGR URL will be used to create the address for POST request

https://myhostname/pegr/api/stats?apiKey= my_pegr_api_key