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kraken-software [2019/07/15 18:10]
aorth
kraken-software [2019/07/15 20:04] (current)
aorth
Line 30: Line 30:
 $ ./​install_kraken2.sh /​export/​apps/​kraken/​2.0.8-beta $ ./​install_kraken2.sh /​export/​apps/​kraken/​2.0.8-beta
 $ sudo chown root /​export/​apps/​kraken/​2.0.8-beta/​*</​code>​ $ sudo chown root /​export/​apps/​kraken/​2.0.8-beta/​*</​code>​
 +
 +Download some [[ftp://​ftp.ccb.jhu.edu/​pub/​data/​kraken2_dbs/​|pre-formatted databases]] and extract them somewhere:
 +
 +<​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.txt · Last modified: 2019/07/15 20:04 by aorth