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import files in Galaxy using the edited files metadata

Now that we have formed the appropriate metadata file, we are going to use it to import the GDC data in a GALAXY User Account. Therefore, you should own a Galaxy account in a Galaxy server, for instance

Import the metadata file in a Galaxy History

  1. Create a new Galaxy history by clicking on the + of the top right menu

  2. Rename you history "TARGET Expression datasets"

  3. Open the upload panel by clicking on the upload icon

  4. Select the Choose local file tab and your edited gdc_sample_sheet.2020-02-19.tsv (see previous section)

  5. Click on Start and close the panel. the edited metadata file should now be in your TARGET Expression datasets history.

Import the expression datasets specified in the metadata file

  1. Click again on the upload icon

  2. This time, select the Paste/Fetch data tab

  3. Click on the Rule-based tab

  4. Select Upload data as: Collection(s), Load tabular data from: History Dataset, Select dataset to load: gdc_sample_sheet.2020-02-19.tsv

    You should see the content of the metadata file appearing.

  5. Click on the Buildbutton

  6. On the left hand side off the panel, there is a "Rules" section, and a link to click on

  7. Then, click a first time on Add Definition and select URL

    You should now see that the column A will be recognized as providing the URLs of the datasets to download.

  8. Click a second time on Add Definition and select List Identifier(s). Further select the B column.

  9. Finish the Rules settings by clicking on Apply

    Now, there is on task remaining: we have to indicate to Galaxy that the first line of the metadata file is the column headers and should not be considered as containing information.

  10. Click on the Filter button,

    select Matching a Supplied Value, from column A (should be already selected), paste 

    File ID
    in the empty field, and finally check the Invert filter checkbox.

    Here is our filter: we do not want to consider lines that contain the string File ID in column A.

  11. Click on Apply button

  12. Finally, give a Name to the future collection of downloaded files, in the field Name. For instance 

    TARGET_AML_FPKMs

    and click the Upload button.

    You should see the following upload banner

    Now, you just need to wait, the upload of the ~200 files, 1.6 GB each, is expected to take less than 5 min.

  13. After completion of the upload, take a look to you dataset collection: