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General Function Checklist


Check IGB file types 

Note: Certain file types created in Galaxy can be opened in IGB by clicking the display in IGB link. Check file types by looking at Galaxy source code. 

  1. Go to https://github.com/galaxyproject/galaxy
  2. Identify and select the current release branch of Galaxy. For example, 18.05 was the current branch in May 2018. 
  3. Navigate the source code directories. Go to display_applications/configs/igb
  4. View list of XML files. Each XML file corresponds to a file type IGB can load from Galaxy. For example, bb.xml lets IGB load bigbed format files.
  5. Check that all file types are listed below. (Note that this list may get out of date as we add support for more file types to Galaxy.)

Open file types 

  1. Go to https://usegalaxy.org
  2. Select Shared Data > Histories
  3. Select and switch to the History named Open Galaxy files in Integrated Genome Browser.
  4. The View in IGB option in Galaxy opens in IGB for the following file formats. Check each of them by opening the file in Galaxy and selecting the View in IGB link. 
    • BED 
    • BAM 
    • BEDGRAPH
    • GTF
    • WIG 
    • BIGWIG 
    • BIGBED

For instructions, see IGB User's Guide. Search for keyword "Galaxy". 

Note: Ask Dr. Loraine to add new files to the History when new file types are supported. These can be uploaded and renamed as required. To support new file types in Galaxy, fork Galaxy and submit a pull request to the latest release branch.

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