Workflow upload

Same as data libraries, you can import workflows, from shared data that has been pre-set in your Galaxy server for this training session.

To access these workflows :

  1. Click the menu Données partagées (Shared data) and select the submenu Workflows. You should see two workflows : paired-data-STAR-RNAseq and paired-data-HISAT2-RNAseq

  2. For each workflow, click on the arrow and select Import.

Now, you'll be able to see these workflows in the Workflow menu.

Running workflows

You need to return to our first galaxy history Inputs, to do so :

  1. Click the menu Utilisateur and select the submenu Historiques sauvegardés.

  2. Click on Inputs. Its status is now current history.

Prepare inputs

These workflows use data collection as inputs, one per condition treat and untreat. Let's create our two data collections !

  1. Click on the checked box.

  2. Select all treated datasets in pair ends :

    • GSM461180_1_treat_paired.fastq.gz
    • GSM461181_1_treat_paired.fastq.gz
    • GSM461180_2_treat_paired.fastq.gz
    • GSM461181_2_treat_paired.fastq.gz

  3. Then click on the button Pour toute la sélection... and Build List of Dataset Pairs.

  4. Enter a name for your dataset collection. Name: Treat data pairs.

  5. Create list

Redo a data collections for untreated datasets.

  1. Unchecked the previous datasets.

  2. Select all untreated datasets in pair ends :

    • GSM461177_1_untreat_paired.fastq.gz
    • GSM461178_1_untreat_paired.fastq.gz
    • GSM461177_2_untreat_paired.fastq.gz
    • GSM461178_2_untreat_paired.fastq.gz

  3. Then click on the button Pour toute la sélection... and Build List of Dataset Pairs.

  4. Enter a name for your dataset collection. Name: Untreat data pairs.

  5. Create list

You are now the happy owner of two dataset paired collections !

It's time to test the worflows !

  1. Go to Menu Workflow.

  2. For the workflow imported: paired-data-HISAT2-RNAseq, click on the arrow and then Run.

  3. History Options

    • Send results to a new history: Yes

  4. 1: treated data pairs: Treat data pairs

  5. 2:GTF: Drosophila_melanogaster.BDGP6.95.gtf.gz

  6. 3: un-treated data pairs: Untreat data pairs

  7. Run workflow

Redo the same for the workflow imported: paired-data-STAR-RNAseq.