kraken-software
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kraken-software [2019/07/15 17:04] – aorth | kraken-software [2023/08/11 09:50] – 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</ | ||
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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: |
< | < | ||
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$ wget ftp:// | $ wget ftp:// | ||
$ for name in *.tgz; do sudo tar xfv " | $ for name in *.tgz; do sudo tar xfv " | ||
+ | |||
+ | Download the larger standard pre-formatted database: | ||
+ | |||
+ | < | ||
+ | $ tar xf k2_standard_20210517.tar.gz | ||
+ | $ sudo mkdir -p / | ||
+ | $ sudo cp database* hash.k2d inspect.txt opts.k2d seqid2taxid.map taxo.k2d / | ||
The '' | The '' |
kraken-software.txt · Last modified: 2023/08/11 10:13 by aorth