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  1. UGENE
  2. UGENE-781

Check external tools for updates

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    Details

    • Type: Task
    • Status: Closed
    • Priority: Major
    • Resolution: Won't Fix
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: Basic-Other
    • Labels:
    • Sprint:
      DEV-11/12/2014, DEV-18/12/2014, DEV-15/01/2015, DEV-22/01/2015, DEV-12/02/2015, DEV-19/02/2015
    • Affect Type:
      Userdefined

      Description

      Check all external tools used in UGENE for new versions available:

      v1.10 tools set:
      CAP3
      Bowtie-0.12.7
      BWA-0.5.9
      blast-2.2.25
      blast-2.2.25+
      clustalw-2.1
      mafft-6.847
      T-Coffee-8.99
      Mr.Bayes-3.2.0
      SPAdes-3.6.0

      built-in tools:
      Muscle, HMMER2, HMMER3, KAlign

        Attachments

          Issue Links

          relates to

          Task - A task that needs to be done. UGENE-4526 Update SPAdes to 3.6.0 version

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

          Task - A task that needs to be done. UGENE-3487 Update BLAST tool to the 2.2.29 version

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. UGENE-3488 Update BLAST+ tool to the 2.2.30 version

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. UGENE-3489 Update Bowtie and Bowtie2

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. UGENE-3490 Update BWA to the 0.7.12 version

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. UGENE-3491 Update MAFFT tool to the 7.212 version

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. UGENE-3492 Update T-Coffee tool to the 11.00 version

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. UGENE-3493 Update MrBayes tool to the 3.2.3 version

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. UGENE-3494 Update SAMTools tool to the 1.0 version

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. UGENE-3495 Update vcftools to the 0.1.12 version

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. UGENE-3828 Update ClustalO to the 1.2.1 version

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. UGENE-860 Update bwa in external tool package to latest version 0.6.1

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

            Activity

              People

              Assignee:
              dkandrov Denis Kandrov
              Reporter:
              mfursov Mikhail Fursov (Inactive)
              Watchers:
              1 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved:

                  Time Tracking

                  Estimated:
                  Original Estimate - 4 days
                  4d
                  Remaining:
                  Remaining Estimate - 4 days
                  4d
                  Logged:
                  Time Spent - Not Specified
                  Not Specified