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--- kraken-software [2019/07/15 15:10] – aorth
+++ kraken-software [2022/03/03 09:05] – aorth
@@ Line 30: / Line 30: @@
 $ ./install_kraken2.sh /export/apps/kraken/2.0.8-beta
 $ 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 "$name" -C /export/data/bio/kraken2/db; done</code>
+Download the larger standard pre-formatted database:
+<code>$ wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20210517.tar.gz
+$ tar xf k2_standard_20210517.tar.gz
+$ sudo mkdir -p /export/data/bio/kraken2/db/standard
+$ sudo cp database* hash.k2d inspect.txt opts.k2d seqid2taxid.map taxo.k2d /export/data/bio/kraken2/db/standard</code>
+The ''kraken2'' application finds these with the ''KRAKEN2_DB_PATH'' environment variable.