This and Exercises 1 and 2 are part of an Galaxy-sponsored free OpenHelix introductory tutorial accessed here.
View history list and then create a workflow from exercises 1 and 2.
1. If you are doing this exercise immediately after exercise 1, the data will be in your history. If not, go to the “Options” pull down menu at the top of the history column and click “Saved Histories.” Your previously created history from exercise 2 will be there. Click on the title and pull down menu, click “Switch” to add history to your current analysis.
The history should look like this (you could import this one to your account by clicking the green "+" icon at the top right in the box below):2. Click “Options” in the right hand History column. Click “Extract Workflow.” Make sure there are 3 steps and that all check boxes (“Treat as input dataset,”Get flanks,” and Extract Genomic DNA) are checked. Type in a workflow name such as “Get SNP flanking” in the workflow name text box and click “Create Workflow.”
3. Your new workflow is now created and you can run this analysis on any similar dataset. Before we look at this workflow and run it, let’sclear the history. Click the Options menu in the right hand History column and click “Create New.” Your history is now cleared. Let’s get some new data to run this analysis on.
Your new workflow should be like this (or you could import this one to your account by clicking the green "+" icon at the top right in the box below)
4. Repeat the steps 1-12 of exercise 1, but this time instead of typing in BRCA1, type in CLOCK and click the first linked result (uc003hba.1) and when naming, name it CLOCK SNPs or something descriptive.
(or you could import this one to your account by clicking the green "+" icon at the top right in the box below)
5. Once the CLOCK SNP data is uploaded to Galaxy, Click the“Workflow” tab at the top of the screen.
6. You will now be at a list of any workflows you’ve created. Click the workflow you just created, “Get SNP Flanking” and choose “Run” in the resulting pull down menu.
7. The workflow steps will now appear in the middle column. In “Step 1: Input dataset,” there will be a pull down menu with your current datasets. Your newly uploaded dataset “Clock SNPs” should be there, choose it if it already isn’t and click “Run Workflow” at the bottom.
8. The workflow will then proceed to do the steps of the analysis you did in exercise 2 automatically on the new dataset! When completed, click the heading of the third dataset “ExtractGenomic DNA on data 2” and view the data. There should be 816 regions and you’ll notice the locations, IDs and sequence. Workflows are great a great method to redo analyses automatically and simply on many datasets.