Installing

To install Krona Tools, 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/. If the bin directory in this path is not already in the PATH environment variable, it will have to be added.
• "--taxonomy <path>" - taxonomy files will be stored in this directory when updateTaxonomy.sh is run. The default is taxonomy/ within the unpacked Krona Tools 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 Krona Tools folder or by pointing to it with this option.

#####Taxonomy database#####

Some tools rely on NCBI taxonomy:

• ktClassifyBLAST
• ktGetTaxIDFromGI
• ktImportBLAST
• ktImportMETAREP-BLAST
• ktImportTaxonomy

To use these tools, updateTaxonomy.sh must be run after installing. This will install the local taxonomy database, which uses about 4 GB of space and requires an additional 12 GB of scratch space during installation. It can also be run later to keep the local database up to date with NCBI.

• 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 (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. Download these files from ftp://ftp.ncbi.nih.gov/pub/taxonomy:
     • gi_taxid_nucl.dmp.gz
     • gi_taxid_prot.dmp.gz
     • taxdump.tar.gz
  • Transfer the files to the taxonomy folder in the standalone KronaTools installation.
  • Run "./updateTaxonomy.sh --local".