help

Format

cg install ?options? ?item? ...

Summary

easy install of optional dependencies (external software used by genomecomb for some analysis) and some reference databases.

Description

cg install makes it easy to install external software and reference databases provided on the genomecomb website by just giving a list of items to be installed to the command. There are 3 types of items:

binaries: binary distributions (application dirs) of software (optionally) used by genomecomb
references: reference directories (genome sequence and all types of annotation)
presets: installs all binaries needed for running the given preset, e.g. ont will install minimap2,sniffles,cutesv,clair3 and modkit

You can get the names of supported items (organized in 3 categaories) by giving the command without arguments:

cg install

By default the binaries are installed in the genomecomb extra directory, making them only available to genomecomb (unless you would put that in the PATH). In the extra directory, they are also the primary choice (overruling installs in other places). refdirs are by default installed The locations can be overruled with the options -bindir and -refdir (bindir should be in PATH for the install to work).

Arguments

item: name/id of software/refdb to install

Options

-refdir directory: reference directories will be installed in the given location
-bindir directory: software/binaries will be installed in the given location

Home

Contact

Installation