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  1. IGB
  2. IGBF-1417

Create new artifact with bigbed and bigwig parsing code from IGV codebase

    Details

    • Story Points:
      2
    • Sprint:
      Fall 2018 Sprint 3, Fall 2018 Sprint 4

      Description

      IGV codebase has updated bigbed and bigwig parsing code.

      We are currently using very old versions of this same code, packaged in artifact bigwig-1.0.jar.

      This older artifact bigwig-1.0.jar uses SeekableStream and SeakableStreamReader classes from another very old artifact - tribble-0.1.jar, which is packaged into the bigwig-1.0.jar artifact.

      However, elsewhere in the project we are now using an htsjdk artifact which contains SeekableStream and SeakableStreamReader classes that can replace same in tribble-0.1.jar. In addition, newer igv code is using these same classes.

      To simplify the code base - and make the final packaged jar files smaller - we will build a new bundle containing IGV bigbed and bigwig parsing code that uses the htsjdk artifact, which will be provided as a bundle by the OSGi framework.

      This new bundle should be as lightweight as possible - it should include just packages we need and include logging code used by the rest of the IGB code base.

      To build the bundle, we will 1st fork the igv code base and add new scripts (or gradle/maven build configuration files) to build the bundle we want. We will also modify the igv code base as required to use our preferred logging framework. We will do this in such a way as to enable us to keep our fork up-to-date with the IGV code base.

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            ann.loraine Ann Loraine added a comment -

            Packages required:

            org.broad.igv.bbfile

            Package may be required - check in IGB code base to be sure:

            org.broad.igv.bigwig

            Show
            ann.loraine Ann Loraine added a comment - Packages required: org.broad.igv.bbfile Package may be required - check in IGB code base to be sure: org.broad.igv.bigwig
            Hide
            kkorey Kiran Korey (Inactive) added a comment -

            Made some code changes to use the new artifact, Please review the changes.
            https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1417-bigwig

            Show
            kkorey Kiran Korey (Inactive) added a comment - Made some code changes to use the new artifact, Please review the changes. https://bitbucket.org/kkorey/kkorey-igb/branch/IGBF-1417-bigwig
            Hide
            ann.loraine Ann Loraine added a comment -

            Check for conflicts. Resolve & then please re-submit pull request.

            Show
            ann.loraine Ann Loraine added a comment - Check for conflicts. Resolve & then please re-submit pull request.
            Hide
            ann.loraine Ann Loraine added a comment -

            bigwig artifact, plus sources, now deployed to

            Show
            ann.loraine Ann Loraine added a comment - bigwig artifact, plus sources, now deployed to https://nexus.bioviz.org/repository/maven-releases/
            Hide
            stiwari8 Srishti Tiwari (Inactive) added a comment -

            Tested on Windows. It works well. The new artifact gets downloaded from the Nexus repository. Bigbed and Bigwig files load properly in IGB.
            Closing.

            Show
            stiwari8 Srishti Tiwari (Inactive) added a comment - Tested on Windows. It works well. The new artifact gets downloaded from the Nexus repository. Bigbed and Bigwig files load properly in IGB. Closing.
            Hide
            ann.loraine Ann Loraine added a comment -

            Repository with revised bigwig / bigbed code is here: https://bitbucket.org/lorainelab/bigwig/src/master/
            Note that the repo contains logic for uploading to maven repositories and packaging as an OSGi bundle.

            Show
            ann.loraine Ann Loraine added a comment - Repository with revised bigwig / bigbed code is here: https://bitbucket.org/lorainelab/bigwig/src/master/ Note that the repo contains logic for uploading to maven repositories and packaging as an OSGi bundle.

              People

              • Assignee:
                stiwari8 Srishti Tiwari (Inactive)
                Reporter:
                ann.loraine Ann Loraine
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                Dates

                • Created:
                  Updated:
                  Resolved: