proteogenomics

Proteogenomics

Files

Workflow: proteogenomics.ga

History file: PSM_Report.tabular

Required Galaxy Tools

If you wish to run the proteogenomics workflow on your own Galaxy instance you will need to install the following, versioned, tools:

Tool Name	Owner	Version
column_maker	devteam	626658afe4cb
fasta_filter_by_length	devteam	2fd6033d0e9c
ncbi_blast_plus	devteam	d724d9af93ee
query_tabular	iuc	1ea4e668bf73
tabular_to_fasta	devteam	0b4e36026794

Workflow Instructions

We have set-up a publically accessible Galaxy instance on the Jetstream cloud-based cyberinfrastructure resource. Here we provide instructions on accessing this public instance.

1. Go to https://z.umn.edu/proteogenomicsgateway

2. Register to use the Galaxy instance. Galaxy requires that all users input an email address to use tools and build workflows etc. To register do the following:

   • Click on the User tab and then click on Register
   • Enter an email address, password and public name of your choosing

NOTE: Users who want to remain anonymous can enter an email in the form of [email protected] (where X is any number of your choosing), along with a password and public name of your choosing. Please note that if the email entered is not valid, the administrators of this instance will not be able to contact the user regarding any issues related to the instance. If the desire it to use this instance for long-term research use, we suggest using a valid email address.

3. Once registered, workflows and sample input data can be accessed within the Shared Data tab.
   • To run the workflow, first appropriate input data must be loaded into your active History. Clickon Shared data and select Histories. From the list of shared Histories, select Input for Query Tabular F1000 Workflow. In the page that appears, select Import History and click on Import when the window appears.
   • Next click on Shared Data, select Workflows
   • When the shared Published Workflows page appears, type Query in the search field
   • The workflow titled Query Tabular F1000: PSM Report ---> Novel Peptides will come up. Click on the drop down arrow on the right of the workflow button, and select Import
   • In the green box that appears, click on Start using this workflow.
   • This will now show up in Your workflows. Click on the dropdown arrow and select Run.
   • The next window will show the steps in the workflow. The first item shows the input data that you just imported into your History that will be processed by the workflow (PSM_report.tabular)
   • Click on Run workflow and the analysis will proceed.