Installing

To install KronaTools, unpack the archive, cd to the resulting directory on a command line, and run ./install.pl. If installing to /usr/local (the default), root privileges will be needed (use "sudo ./install.pl" in OS X).

Options for install.pl:

• "--prefix <path>" - scripts will be installed in the bin directory within this path. The default is /usr/local/.
• "--taxonomy <path>" - taxonomy files will be stored in this directory when updateTaxonomy.sh or updateAccessions.sh is run. The default is taxonomy/ within the unpacked KronaTools directory. If the taxonomy database was installed in a previous version of Krona Tools, it can be reused by moving it to the to new KronaTools folder or by pointing to it with this option.

Taxonomy database

Some tools rely on NCBI taxonomy:

• ktClassifyBLAST
• ktGetLCA
• ktGetTaxInfo
• ktImportBLAST
• ktImportMETAREP-BLAST
• ktImportTaxonomy

To use these tools, updateTaxonomy.sh must be run after installing. This will install the local taxonomy database, which uses less than 100Mb of disk space and should take a few minutes or less to run. It can also be run later to keep the local database up to date with NCBI.

Accession database

Additionally, some tools rely on accession-to-taxonomyID lookups:

• ktClassifyBLAST
• ktGetTaxIDFromAcc
• ktImportBLAST

To use these tools, updateAccessions.sh must be run after installing. This will install the local accession-to-taxonomyID database, which uses about 16 GB of disk space and an additional 16 GB of scratch space during installation (at the time of this writing; it is always growing) and takes minutes or up to an hour to run. It can also be run later to keep the local database up to date with NCBI.

Notes for database updates

• curl, which is included in OS X and most Linux distributions, is required for automatic downloads.
• To install the taxonomy database in a location other than the one used during installation (see install.pl options above), the full path to the custom directory can be given as an argument to updateTaxonomy.sh or updateAccessions.sh (e.g. ./updateTaxonomy.sh /path/to/taxonomy). The custom taxonomy can then be used during import by specifying -tax /path/to/taxonomy to the import command being used.
• For installations with no internet connection:
  1. Retrieve the necessary source files from NCBI
     • Automatic download
       1. Download and untar KronaTools on an internet-connected computer (running install.pl is not necessary).
       • Run ./updateTaxonomy.sh --only-fetch. The files will be downloaded to KronaTools/taxonomy.
       • If accession lookups are needed, also run ./updateAccessions.sh --only-fetch.
     • OR Manual download
       • Taxonomy
         • taxdump.tar.gz
       • Accessions (place in <KronaTools>/taxonomy/accession2taxid/)
         • dead_nucl.accession2taxid.gz
         • dead_prot.accession2taxid.gz
         • dead_wgs.accession2taxid.gz
         • nucl_gb.accession2taxid.gz
         • nucl_wgs.accession2taxid.gz
         • prot.accession2taxid.gz
  2. Transfer the source files from the internet-connected computer to the KronaTools/taxonomy directory on the target computer.
  3. On the target computer, run ./updateTaxonomy.sh --only-build
  4. If accession lookups are needed, run ./updateAccessions.sh --only-build.