Now that you are familiar with manipulations in Galaxy with the Use Cases 1-1 to 1-4 described in detail in the previous chapters, we will describe the other Use Case analyses more concisely. If you experience lack of skills in basic Galaxy operations (tool usage, copy of datasets, etc), do not hesitate to go back and examine the previous chapters step by step.

Input data for Use Case 3-1

As for the previous Use Cases 1 and 2, the first step is to collect all the input data in a history that we will name Input data for Use Case 3-1.

  1. Create a new history
  2. Rename this history Input data for Use Case 3-1

  3. We are going to upload 40 datasets form the EBI ENA SRP068722. This is a bit tedious, but if you follow the instructions bellow, it is not difficult.

    • Use the tool Extract reads in FASTQ/A format from NCBI SRA, fill the SRR accession field with the first EBI SRA identifier SRR3111582 and let the output format selected as fastq. Click the Execute button.
    • Now that the tool has started to run, you can click on the dataset in order to expand the information. Then click on the rerun icon (two curved arrows, when the mouse passes over the icon you can see the info "Run this job again" popping up). The only thing you have to do is to edit the SRR accession field from SRR3111582 to SRR3111583, and press the Execute button.
    • Just repeat this operation with all the datasets we want to upload. Here is the full list of the SRR identifiers for the 40 datasets we will upload. Note that these identifiers increment by 1 from SRR3111582 to SRR3111622 with one exception: we go directly from SRR3111614 to SRR3111616.

    SRR3111582 SRR3111583 SRR3111584 SRR3111585 SRR3111586 SRR3111587 SRR3111588 SRR3111589 SRR3111590 SRR3111591 SRR3111592 SRR3111593 SRR3111594 SRR3111595 SRR3111596 SRR3111597 SRR3111598 SRR3111599 SRR3111600 SRR3111601 SRR3111602 SRR3111603 SRR3111604 SRR3111605 SRR3111606 SRR3111607 SRR3111608 SRR3111609 SRR3111610 SRR3111611 SRR3111612 SRR3111613 SRR3111614 SRR3111616 SRR3111617 SRR3111618 SRR3111619 SRR3111620 SRR3111621 SRR3111622

  4. For each of the 40 imported datasets, click the pencil icon, and change the datatype to fastqsanger. Be systematic, do it for all datasets 1 to 40.

  5. Click on the checked box icon in the history's top menu, check all 40 datasets (All button), and For all selected, Build a dataset list that you name "SRP068722".
  6. Copy the vir1 nucleotide BLAST database from the References history to the current history Input data for Use Case 3-1.
  7. Now we still have to associate sequencing dataset coming from the same patient. We are going to use the tool Concatenate multiple datasets to merge multiple datasets in a fastq file.
    • For patient 0450-318, use Concatenate multiple datasets and select the datasets SRR3111582 to SRR3111587. Run the tool and rename the dataset "patient 0450-318"
    • For patient 0387-272, use Concatenate multiple datasets and select the datasets SRR3111588 to SRR3111593. Run the tool and rename the dataset "patient 0387-272"
    • For patient 0629-453, use Concatenate multiple datasets and select the datasets SRR3111594 to SRR3111599. Run the tool and rename the dataset "patient 0629-453"
    • For patient 0444-312, use Concatenate multiple datasets and select the datasets SRR3111600 to SRR3111603. Run the tool and rename the dataset "patient 0444-312"
    • For patient 0500-355neg, use Concatenate multiple datasets and select the datasets SRR3111604 and SRR3111605. Run the tool and rename the dataset "patient 0500-355neg"
    • For patient 0292-xxxneg, use Concatenate multiple datasets and select the datasets SRR3111606 and SRR3111607. Run the tool and rename the dataset "patient 0292-xxxneg"
    • For patient 0394-274, use Concatenate multiple datasets and select the datasets SRR3111608 and SRR3111609. Run the tool and rename the dataset "patient 0394-274"
    • For patient 0218-162neg, use Concatenate multiple datasets and select the datasets SRR3111610 and SRR3111611. Run the tool and rename the dataset "patient 0218-162neg"
    • For patient 0311-217HIVneg, use Concatenate multiple datasets and select the datasets SRR3111612 and SRR3111613. Run the tool and rename the dataset "patient 0311-217HIVneg"
    • For patient 0440-307neg, use Concatenate multiple datasets and select the datasets SRR3111614 and SRR3111616. Run the tool and rename the dataset "patient 0440-307neg"
    • For patient 0518-370neg, use Concatenate multiple datasets and select the datasets SRR3111617 and SRR3111618. Run the tool and rename the dataset "patient 0518-370neg"
    • For patient 0560-420neg, use Concatenate multiple datasets and select the datasets SRR3111619 and SRR3111620. Run the tool and rename the dataset "patient 0560-420neg"
    • For patient 0575-419neg, use Concatenate multiple datasets and select the datasets SRR3111621 and SRR3111622. Run the tool and rename the dataset "patient 0575-419neg"
  8. The last action to perform in this history is to create a dataset collection of patient datasets: Click on the checked box icon in the history's top menu, check the "patient... " datasets we have just generated by concatenation (13 datasets), and For all selected, Build a dataset list that you name "patient collection".
  9. We are done.

History for Use Case 3-1

  1. Stay in the history Input data for Use Case 3-1
  2. pick the workflow Metavisitor: Workflow for Use Case 3-1 in the workflows menu, and select the run option.
  3. For Step 1 (Fever Patient Sequences collection), select patient collection (this should be already selected).
  4. For Step 2, select the nucleotide vir1 blast database (this should also be already selected)
  5. As usual, check the box Send results to a new history, edit the name of the new history to History for Use Case 3-1, and Execute the workflow ! Note, that for complex workflows with dataset collections in input, the actual warning that the workflow is started may take time to show up.