kraken-software
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| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| kraken-software [2022/03/03 09:05] – aorth | kraken-software [2023/08/11 10:13] (current) – aorth | ||
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| ===== Information ===== | ===== Information ===== | ||
| - | * Version: 2.0.8-beta | + | * Version: 2.1.2 |
| * Added: August, 2016 | * Added: August, 2016 | ||
| - | * Updated: July, 2019 | + | * Updated: July, 2022 |
| * Link: https:// | * Link: https:// | ||
| ===== Usage ===== | ===== Usage ===== | ||
| - | See which versions | + | See which versions are available: |
| < | < | ||
| Load one version into your environment and run it: | Load one version into your environment and run it: | ||
| - | < | + | < |
| $ kraken2 --help</ | $ kraken2 --help</ | ||
| Line 23: | Line 23: | ||
| Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
| - | < | + | < |
| - | $ cd kraken2 | + | $ git clone https:// |
| - | $ git checkout v2.0.8-beta | + | $ git checkout v2.1.2 |
| - | $ sudo mkdir -p / | + | $ sudo mkdir -p / |
| - | $ sudo chown aorth / | + | $ sudo chown aorth / |
| - | $ ./ | + | $ ./ |
| - | $ sudo chown root / | + | $ sudo chown root / |
| - | Download some [[ftp://ftp.ccb.jhu.edu/ | + | Download some [[https://benlangmead.github.io/aws-indexes/k2|pre-formatted databases]] and extract them somewhere: |
| - | < | + | < |
| - | $ wget ftp://ftp.ccb.jhu.edu/pub/data/ | + | $ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Greengenes13.5_20200326.tgz |
| - | $ wget ftp://ftp.ccb.jhu.edu/pub/data/ | + | $ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Silva132_20200326.tgz |
| - | $ wget ftp://ftp.ccb.jhu.edu/ | + | $ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Silva138_20200326.tgz |
| $ for name in *.tgz; do sudo tar xfv " | $ for name in *.tgz; do sudo tar xfv " | ||
| - | Download | + | Download |
| - | < | + | < |
| - | $ tar xf k2_standard_20210517.tar.gz | + | $ wget https://genome-idx.s3.amazonaws.com/ |
| - | $ sudo mkdir -p /export/data/ | + | |
| - | $ sudo cp database* hash.k2d inspect.txt opts.k2d seqid2taxid.map taxo.k2d / | + | |
| The '' | The '' | ||
kraken-software.1646298357.txt.gz · Last modified: 2022/03/03 09:05 by aorth