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  1. UGENE
  2. UGENE-5874

Integrate CLARK as an external tool

    Details

    • Type: New Feature
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: 1.28
    • Fix Version/s: 1.31
    • Component/s: Basic-Other, NGS
    • Labels:
    • Environment:

      Linux, Mac OS X

    • Story Points:
      5
    • Epic Link:
    • Sprint:
      DEV-29-2, DEV-29-3
    • Affect Type:
      Userdefined

      Description

      On the "External Tools" page in the Application Settings add a new group called "CLARK". The group should have the following sub-items: "set_targets.sh", "classify_metagenome.sh", "CLARK", "CLARK-l".

      Add these tools to the Linux and Mac OS X external tools packages (the tools are not available on Windows).

      Use description of the group and the sub-items from the specification. Don't forget to provide other information as well: the tool version and the binary path.

        Attachments

          Issue Links

          blocks

          New Feature - A new feature of the product, which has yet to be developed. UGENE-5888 Online installer: CLARK component and license

          • Critical - Crashes, loss of data, severe memory leak.
          • Closed

            Activity

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            atiunov Aleksey Tiunov [X] (Inactive) added a comment -

            The version of tools are set only for CLARK and CLARK-l binaries, because other utility tools don't provide their version.
            The subitems list in the issue description and specification differs. Currently, the group contains the next subitems: builddb.sh, getTargetsDef, getfilesToTaxNodes, getAccssnTaxID, CLARK, CLARK-l. This list fits the specification, the issue description is outdated.
            The description of CLARK and CLARK-l items slightly differs from the specification: the first sentence is "One of the classifiers from the CLARK framework." instead of "One of the classifiers from the CLARK framework, may be called by the “classify_metagenome.sh” script." for both tools. It is better, because "classify_metagenome.sh" script is not included into the package.

            Show
            atiunov Aleksey Tiunov [X] (Inactive) added a comment - The version of tools are set only for CLARK and CLARK-l binaries, because other utility tools don't provide their version. The subitems list in the issue description and specification differs. Currently, the group contains the next subitems: builddb.sh, getTargetsDef, getfilesToTaxNodes, getAccssnTaxID, CLARK, CLARK-l. This list fits the specification, the issue description is outdated. The description of CLARK and CLARK-l items slightly differs from the specification: the first sentence is "One of the classifiers from the CLARK framework." instead of "One of the classifiers from the CLARK framework, may be called by the “classify_metagenome.sh” script." for both tools. It is better, because "classify_metagenome.sh" script is not included into the package.
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            yalgaer Yuliya Algaer added a comment -

            Reviewed

            Show
            yalgaer Yuliya Algaer added a comment - Reviewed

              People

              Assignee:
              varlax Alexey Varlamov
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Aleksey Tiunov [X] (Inactive)
              Watchers:
              2 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: