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  1. UGENE
  2. UGENE-6039

Unify "Database" parameters in the "build" and "classify" workflow elements

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      Description

      To make work with the database parameters consistent in different NGS reads classification workflow elements the following modifications are required:

      1. Rename the "Database URL" parameter of the "Build CLARK Database" element to "Database".
      2. Rename parameters of the "Build Kraken Database" element:
        • "New database name" > "Database"
        • "Input database name" > "Input database" (the parameter is shown when "Shrink" mode is selected).
      3. Currently database files are store is a tool folder. Add additional subfolders for the database. Thus, the "ngs_classification" folders structure, created by the installer, should be the following:
        / ngs_classification
          /clark
            /viral_database
            /bacteria_viral_database  
          /diamond
            /uniref
          /kraken
            /minikraken
          /refseq
           ...
          /taxonomy
           ...
        
      4. If the corresponding data are available (= have been downloaded), specify default values for "classify" elements (leave an empty value, if the data are not available):
        • For Kraken-classify - the "minikraken" folder.
        • For CLARK-classify - the "bacteria_viral_database" folder. If it is not present, "viral_database".
        • For DIAMOND-classify - the "uniref/uniref50.dmnd" file. If it is not present, "uniref/uniref90.dmnd".
      5. A custom dialog appear when selecting the database parameter for all three "build" elements and CLARK-classify. Replace this dialog by a common dialog.
      6. Optionally, fix the issue, specified in UGENE-5835 comment (files inside a folder are not visible on Linux, on Mac OS X it's OK):

        database setup is unclear - one cannot see the folders content

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              Assignee:
              atiunov Aleksey Tiunov [X] (Inactive)
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Dmitrii Sukhomlinov
              Watchers:
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                Dates

                Created:
                Updated:
                Resolved: