Skip to content

Running a workflow in Galaxy

In this use case, we are going to

  • Upload 3 workflow description files in the Galaxy server instance
  • Visualise these workflows and see that tools to execute the workflows are missing
  • since you are administrating the instance, install the missing tools
  • Eventually run the workflows on input data obtained from a remote public repository.

1. Upload workflow description file (.ga)

  • Ensure you are connected to your Galaxy server as an admin (the email you have entered in the galaxy.yml configuration file and the password to you've entered for this login when you registered for the first time)
  • Click the workflow menu
  • Click the "Upload or import workflow" button at the top right

  • In the Galaxy workflow URL: field, paste the url of the workflow file: 

    https://raw.githubusercontent.com/ARTbio/Run-Galaxy/master/workflows/Galaxy-Workflow-canonical_transposons.gtf_from_transposon_sequence_set.txt.ga
    Note that this file is in the Run-Galaxy repository where a part of the material for this training is hosted

  • Click on the Import button

  • repeat the same operation with the second workflow 

    https://raw.githubusercontent.com/ARTbio/Run-Galaxy/master/workflows/Galaxy-Workflow-Extract_canonical_transposons_fasta.ga

  • repeat the same operation with the third workflow 

    https://raw.githubusercontent.com/ARTbio/Run-Galaxy/master/workflows/Galaxy-Workflow-workflow_of_workflows.ga

Note

Alternatively, you could upload the workflow files from you computer instead of uploading them by URL

  • the Workflow menu is now a list of 3 workflows that should look like :

imported workflow

  • Click the workflow canonical_transposons.gtf from transposon_sequence_set.txt (imported from uploaded file) and the Edit option
  • Observe the warning window that should look like:
Issues loading this workflow

Please review the following issues, possibly resulting from tool upgrades or changes.

  • Step 3: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1
    • Tool is not installed
  • Step 4: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1
    • Tool is not installed
  • Step 5: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1
    • Tool is not installed
  • Step 6: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1
    • Tool is not installed
  • Step 7: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1
    • Tool is not installed
  • Step 9: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1
    • Tool is not installed

When you read the warnings, you will see that the workflow was indeed successfully imported. However, some tools are missing, namely: 

toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1/1.0.1
toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.1
The other lines are redundant, because the workflow is using the same tools at different steps.

Click on the Continue button. You should now see missing tools in red and missing links between various workflow steps. Note that some tools are indeed present because they are installed by default in the provided Galaxy framework.

broken workflow

broken workflow

  • We are going to fix this. Click on the Continue button and then the upper "wheel" icon and select Close, we will come back to the workflow editor when the missing tools are installed in the server.

2. Installing (missing) tools

The missing tools are reported in the tools.yml file in yaml format in the Run-Galaxy repository, as well as just bellow.

Details of missing tools

Thus, we have to install the following missing tool in our Galaxy instance:

tools: 

- name: regex_find_replace
  owner: galaxyp
  tool_panel_section_label: Analyse des genomes
  tool_shed_url: https://toolshed.g2.bx.psu.edu

  • Click on the Admin top menu
  • In the left bar click on Manage tools

Check that there is actually no installed tools !

  • Now, click the Install new tools menu (again in the left bar)
  • Press the Galaxy Main Tool Shed button
  • In the search field, copy and paste 
    regex_find_replace
    and press the Enter key.
  • Two tools will show up, one owned by jjohnson and the other owned by galaxyp. We want to install the latter one, click on it and select install button of the lattest revision (2, version 1.0.1)
  • In the Target Section: menu, select Text Manipulation. Thus, the tool will appears in the section Text Manipulation of the Galaxy tools.
  • Click OK
  • After a few seconds, you will notice the Cloning... then soon Installing dependencies displayed by the install button.
  • And rapidly enough, the Install button should turn to a red Uninstall button.
  • You can now check the Installed only circle at the top, and look at the newly installed tool regex_find_replace in the list.

3. Check that the imported workflows now display correctly

If you click the workflow top menu, you should now be able to edit the imported workflows, and see that everything is displaying correctly. For the workflow canonical_transposons.gtf from transposon_sequence_set.txt :

clean workflow

We can go through the various steps of the workflows and figure out what they are doing.

This first workflow performs a suite of find-and-replace text manipulations, starting from input data that has been tagged transposon_set_embl.txt and producing a new text dataset that is renamed canonical_transposons.gtf.

The second workflow uses the same input data file transposon_set_embl.txt to generate a fasta file of canonical_transposon sequences

The third workflow is a workflow of the two previous workflows !

We will come back to all these steps after the workflows execution. However, we need to retrieve the input data set before running the workflows on these data.

4. Retrieve the transposon_set_embl.txt dataset

  • Create a new history and name it transposon_set_embl.txt manipulation

  • import the dataset using the Paste/Fetch data mode of the upload manager (the small bottom-top arrow icon at the top left of the Galaxy interface). Copy the URL 

    https://github.com/bergmanlab/transposons/raw/2018c2e848cec2aefc4a87187d5ed5927d04c9a4/current/transposon_sequence_set.embl.txt
    in the open field and click the Start button.

  • have a close look at the file

5. Run the workflow

  • Click on the workflow menu
  • Click on the first workflow and select the Run option
  • Leave the Send results to a new history menu to the No option for the moment.
  • Just Click the Run workflow button to run the workflow, and look at datasets in the history turning from grey to yellow to green. Note: often you don't see the dataset in the "yellow" state (running). You just need to refresh the history with the 2-curved-arrows icon of the local history menu.
  • repeat the same operation (from the input history) for the second workflow Extract canonical transposons fasta (imported from uploaded file)

Discussion on workflows and on workflow of workflows

6. Stop and destroy your bare-galaxy instance

Since we are now at the end of the first use case, we can destroy the VM instance.

  • Go to you Google Cloud Platform management web page.
  • Select your bare-galaxy VM
  • roll-down the top menu with the 3 vertical dots, and select Supprimer