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Galaxy

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Created by Ivory Blakley, last modified by Ann Loraine on May 30, 2018

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General Function Checklist

Check IGB file types

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.
- Go to https://github.com/galaxyproject/galaxy
- Identify and select the current release branch of Galaxy. For example, 18.05 was the current branch in May 2018.
- Navigate the source code directories. Go to display_applications/igb
- View list of XML files. Each XML file enables IGB to open a file type. For example, bb.xml enables IGB to open a bigbed file hosted on a Galaxy server.
- Check that all file types are listed below.

Open file types

Go to https://usegalaxy.org
- Select Shared Data > Histories
- Search for user aloraine
- Select History named For Testing IGB to Galaxy Bridge

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
For instructions, see IGB User's Guide.

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