General Function Checklist

Check IGB file types 

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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. 

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1. Go to https://github.com/galaxyproject/galaxy

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2. Identify and select the current release branch of Galaxy. For example, 18.05 was the current branch in May 2018. 

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2. Navigate the source code directories. Go to display_applications/configs/igb

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2. View list of XML files. Each XML file

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1. corresponds to

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1. a file type IGB can load from Galaxy. For example, bb.xml

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1. lets IGB

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1. load bigbed format files.
2. Check that all file types are listed below

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1. . (Note that this list may get out of date as we add support for more file types to Galaxy.)

Open file types 

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1. Go to https://usegalaxy.org

•  Select Shared Data > Histories
•  Search for user aloraine
•  Select History named For Testing IGB to Galaxy Bridge

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•    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 
  •  GTF 
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•  For instructions, see IGB User's Guide. 

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2. Click Data > Histories.
3. Click Public Histories.
4. Where it says "search histories", type: Open Galaxy files in Integrated Genome Browser
5. Click on the search result, then click View.
6. Check that each of the following file formats can be opened in IGB via the display in IGB link. For more detailed instructions, see View Galaxy files in IGB.

• •  BAM
  •  BIGBED
  •  BED
  •  BEDGRAPH
  •  BIGWIG
  •  GTF
  •  WIG 

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.