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kraken-software [2016/08/16 08:21]
joguya created
kraken-software [2019/07/15 20:04] (current)
aorth
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 ===== Information ===== ===== Information =====
  
-  * Version: ​0.10.5+  * Version: ​2.0.8-beta
   * Added: August, 2016   * Added: August, 2016
-  * Link: https://​ccb.jhu.edu/​software/​kraken/+  ​* Updated: July, 2019 
 +  ​* Link: https://​ccb.jhu.edu/​software/​kraken2/
  
 ===== Usage ===== ===== Usage =====
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 <​code>​$ module avail kraken</​code>​ <​code>​$ module avail kraken</​code>​
  
-Load kraken +Load one version into your environment and run it: 
-<​code>​$ module load kraken/0.10.5</​code>​+<​code>​$ module load kraken/2.0.8-beta 
 +$ kraken2 --help</​code>​
  
 ===== Installation ====== ===== Installation ======
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 Notes from the sysadmin during installation:​ Notes from the sysadmin during installation:​
  
-<​code>​ +<​code>​$ ​git clone https://​github.com/​DerrickWood/​kraken2.git 
-cd /tmp/ +cd kraken2 
-$ wget https://​github.com/​DerrickWood/​kraken/​archive/​v0.10.5-beta.tar.gz +git checkout v2.0.8-beta 
-tar -xvf v0.10.5-beta.tar.gz +$ sudo mkdir -p /​export/​apps/​kraken/​2.0.8-beta 
-cd kraken-0.10.5-beta/ +$ sudo chown aorth /​export/​apps/​kraken/​2.0.8-beta 
-$ sudo mkdir -p /​export/​apps/​kraken/​0.10.5/ +$ ./install_kraken2.sh /​export/​apps/​kraken/​2.0.8-beta 
-$ sudo chown joguya:​joguya ​/​export/​apps/​kraken/​0.10.5/ +$ sudo chown root /​export/​apps/​kraken/​2.0.8-beta/​*</​code>​ 
-$ scl enable devtoolset-2 bash + 
-$ ./install_kraken.sh /​export/​apps/​kraken/​0.10.5/ +Download some [[ftp://ftp.ccb.jhu.edu/pub/​data/​kraken2_dbs/​|pre-formatted databases]] and extract them somewhere:​ 
-$ sudo chown -R root:root /​export/​apps/​kraken/​0.10.5+ 
-</​code>​+<​code>​$ sudo mkdir -p /​export/​data/​bio/​kraken2/​db 
 +$ wget ftp://​ftp.ccb.jhu.edu/​pub/​data/​kraken2_dbs/​16S_Greengenes_20190418.tgz 
 +$ wget ftp://​ftp.ccb.jhu.edu/​pub/​data/​kraken2_dbs/​minikraken2_v1_8GB_201904_UPDATE.tgz 
 +$ wget ftp://​ftp.ccb.jhu.edu/​pub/​data/​kraken2_dbs/​minikraken2_v2_8GB_201904_UPDATE.tgz 
 +$ for name in *.tgz; do sudo tar xfv "​$name"​ -C /​export/​data/​bio/​kraken2/​db;​ done</​code>​ 
 + 
 +The ''​kraken2''​ application finds these with the ''​KRAKEN2_DB_PATH''​ environment variable.
kraken-software.1471324915.txt.gz · Last modified: 2016/08/16 08:21 by joguya