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Type: Improvement
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Status: Closed
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Priority: Blocker
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Resolution: Fixed
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Affects Version/s: 1.31.1
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Fix Version/s: 1.32
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Component/s: Basic-Other, NGS
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Labels:
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Environment:
macOS, Linux 64-bit
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Story Points:3
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Tests Type:Untestable
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Epic Link:
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Sprint:DEV-32-3
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Affect Type:Userdefined
Online installers on macOS and Linux 64-bit should be modified:
- 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).
- Parent component "Classification with MetaPhlAn2" with description:
- On the "License Agreement" page of the installer add "MetaPhlAn2" license. Use the "license.txt" file from
UGENE-6252.
- relates to
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UGENE-6254 Add "Classify Sequences with MetaPhlAn2" workflow element
- Closed
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UGENE-6252 Add MetaPhlAn2 files to Linux 64-bit and macOS external tools packages
- Closed
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UGENE-6265 Use "mpa_v20_m200" (if available) in the MetaPhlAn2 workflow element
- Closed