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Type: Improvement
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Status: Closed
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Priority: Critical
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Resolution: Fixed
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Affects Version/s: virogenesis
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Fix Version/s: 1.31
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Labels:
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Story Points:3
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Epic Link:
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Sprint:DEV-30-5
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Affect Type:Userdefined
To make work with the database parameters consistent in different NGS reads classification workflow elements the following modifications are required:
- Rename the "Database URL" parameter of the "Build CLARK Database" element to "Database".
- 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).
- 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 ...
- 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".
- A custom dialog appear when selecting the database parameter for all three "build" elements and CLARK-classify. Replace this dialog by a common dialog.
- Optionally, fix the issue, specified in
UGENE-5835comment (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
- is duplicated by
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UGENE-6013 Rename folder to "minikraken"
- Closed
- relates to
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UGENE-5835 Add “Classify Sequences with Kraken” workflow element
- Closed
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UGENE-6265 Use "mpa_v20_m200" (if available) in the MetaPhlAn2 workflow element
- Closed