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  1. UGENE
  2. UGENE-6264

Online installer: MetaPhlAn2 component and license, mpa_v20_m200 database

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Blocker
    • Resolution: Fixed
    • Affects Version/s: 1.31.1
    • Fix Version/s: 1.32
    • Component/s: Basic-Other, NGS
    • Labels:
    • Environment:

      macOS, Linux 64-bit

    • Story Points:
      3
    • Tests Type:
      Untestable
    • Epic Link:
    • Sprint:
      DEV-32-3
    • Affect Type:
      Userdefined

      Description

      Online installers on macOS and Linux 64-bit should be modified:

      1. On the "Select Components" page of the installers add the following components (between "DIAMOND" and "WEVOTE"):
        • Parent component "Classification with MetaPhlAn2" with description:
          MetaPhlAn2 (METAgenomic PHyLogenetic ANalysis) is a tool for taxonomy classification of metagenomic NGS data. It relies on ~1M unique clade-specific marker genes.
          
        • Child component "MetaPhlAn2 external tools" installs executable from UGENE-6252: "metaphlan2.py" and "utils/read_fastx.py". They should be put to ".../tools/metaphlan2-2.7.7" subfolder of the UGENE package. The description of the component should be:
          Check this item to install MetaPhlAn2 executables.
          
        • Child component "Marker database (mpa_v20_m200)" provides the database files. See UGENE-6254 ("database can be found on the file server in folder "/data/test_data/UGENE-6254/mpa_v20_m200"). The database files should be put to ".../data/ngs_classification/metaphlan2/mpa_v20_m200" subfolder of the UGENE package. The description of the component should be:
          A database with ~1M unique clade-specific marker genes identified from ~17,000 reference genomes (~13,500 bacterial and archaeal, ~3,500 viral, and ~110 eukaryotic).
          
      2. On the "License Agreement" page of the installer add "MetaPhlAn2" license. Use the "license.txt" file from UGENE-6252.

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              Assignee:
              kir Kirill Rasputin
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Aleksey Tiunov [X] (Inactive)
              Watchers:
              1 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: