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kraken-software [2019/07/15 15:10] aorthkraken-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://ccb.jhu.edu/software/kraken2/   * Link: https://ccb.jhu.edu/software/kraken2/
  
 ===== Usage ===== ===== Usage =====
  
-See which versions of kraken are available:+See which versions are available:
 <code>$ module avail kraken</code> <code>$ module avail kraken</code>
  
 Load one version into your environment and run it: Load one version into your environment and run it:
-<code>$ module load kraken/2.0.8-beta+<code>$ module load kraken/2.1.2
 $ kraken2 --help</code> $ kraken2 --help</code>
  
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 Notes from the sysadmin during installation: Notes from the sysadmin during installation:
  
-<code>$ git clone https://github.com/DerrickWood/kraken2.git +<code>$ cd /tmp 
-$ cd kraken2 +$ git clone https://github.com/DerrickWood/kraken2.git 
-$ git checkout v2.0.8-beta +$ git checkout v2.1.2 
-$ sudo mkdir -p /export/apps/kraken/2.0.8-beta +$ sudo mkdir -p /export/apps/kraken/2.1.2 
-$ sudo chown aorth /export/apps/kraken/2.0.8-beta +$ sudo chown aorth /export/apps/kraken/2.1.2 
-$ ./install_kraken2.sh /export/apps/kraken/2.0.8-beta +$ ./install_kraken2.sh /export/apps/kraken/2.1.2 
-$ sudo chown root /export/apps/kraken/2.0.8-beta/*</code>+$ sudo chown root /export/apps/kraken/2.1.2/*</code> 
 + 
 +Download some [[https://benlangmead.github.io/aws-indexes/k2|pre-formatted databases]] and extract them somewhere: 
 + 
 +<code>$ cd /var/scratch 
 +$ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Greengenes13.5_20200326.tgz 
 +$ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Silva132_20200326.tgz 
 +$ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Silva138_20200326.tgz 
 +$ for name in *.tgz; do sudo tar xfv "$name" -C /export/data/bio/kraken2/db; done</code> 
 + 
 +Download several larger databases (careful about space!): 
 + 
 +<code>$ wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20230605.tar.gz 
 +$ wget https://genome-idx.s3.amazonaws.com/kraken/k2_nt_20230502.tar.gz</code> 
 + 
 +The ''kraken2'' application finds these with the ''KRAKEN2_DB_PATH'' environment variable.
kraken-software.1563203444.txt.gz · Last modified: 2019/07/15 15:10 by aorth