Uploaded image for project: 'UGENE'
  1. UGENE
  2. UGENE-6098

Integrate StringTie as an external tool

    XMLWordPrintable

    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: virogenesis
    • Fix Version/s: 1.31
    • Component/s: Basic-Other, NGS
    • Environment:

      Linux 64-bit, Mac OS X

    • Story Points:
      3
    • Epic Link:
    • Sprint:
      DEV-31-1
    • Affect Type:
      Userdefined

      Description

      StringTie (https://ccb.jhu.edu/software/stringtie/) is a C++ application. By default, executables for Linux 64-bit and macOS are only distributed. So, integrate it into the corresponding UGENE packages only for now. The tool has "Artistic License". Thus, it is allowed to distribute the StringTie package.

      Note for future: it is NOT allowed to distribute a modified version of the package!

      The integration includes:

      • Add a new item "StringTie" to the "External Tools" page in the Application Settings. It should have the following description:
        StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.
        
      • Specify "Version" and "Binary path" below like in other external tools descriptions.
      • Use the "stringtie" executables from the x68_64 Linux and macOS tar.gz packages. Add it to all external tools packages.
      • On the "Select Components" page of online installer add "StringTie" item to the "Full package additions (include some NGS tools)/External tools" group.
      • On the "License Agreement" page add the license. The license file is available in the tar.gz packages.

        Attachments

          Issue Links

            Activity

              People

              Assignee:
              atiunov Aleksey Tiunov [X] (Inactive)
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Dmitrii Sukhomlinov
              Watchers:
              1 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: