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  1. UGENE
  2. UGENE-2286

Remove HMMER3 from source code and create an external tool

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Minor
    • Resolution: Fixed
    • Affects Version/s: 1.12.3
    • Fix Version/s: None
    • Component/s: Basic-Nucl, Basic-Protein
    • Labels:
    • Story Points:
      8
    • Tests Type:
      Functional/Unit
    • Sprint:
      DEV-23-1, DEV-23-2, DEV-24-1, DEV-23-3 (additional)
    • Affect Type:
      Userdefined

      Description

      HMMER3 is currently embedded into the UGENE source code. Its version is quiet old. The old HMMER3 source code should be removed and corresponding external tool should be added instead.

      Note that it is better to add "Sequence database" input field in the HMMER search dialog. This is required because the input file may be a very big multi-FASTA file and it will take time to open it in GUI.

      Consider also addition of other tools from the HMMER3 package into UGENE.

        Attachments

          Issue Links

          relates to

          Improvement - An improvement or enhancement to an existing feature or task. UGENE-5282 HMMER 3: build and phmmer via WD

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. UGENE-5174 Sometimes program crashes when build HMMER3 profile

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. UGENE-5281 HMMER 3: wrong range for --domE

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. UGENE-5283 Update HMMER 3 code to 3.1b2

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

            Activity

              People

              Assignee:
              kir Kirill Rasputin
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Denis Kandrov
              Watchers:
              7 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: