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2. Basic Usage
This page details basic usage for getphylo.
The easiest way to run getphylo for the first time is to navigate to the folder containing some .gbk files and typing:
getphylo
This will run getphylo with default settings.
Note: By default, getphylo will will look for files with the extension '.gbk'. If your files have other extensions you can point to them with -g - see below
If you want to point to a list of files other that '.gbk', you can point with -g. You should use '*' as a wildcard and make sure that the string is in quotations!
getphylo -g 'input/*.myfiles.gb'
By default, getphylo will save its results into a new directory ./output. You can specify a new output directory with -o. If the directory does not exist, getphylo will create it!
getphylo -o ~/custom_directory/output_1
By default, getphylo will not print to the terminal. If you want to watch getphylo as it progresses you will need to set a logging level with -l.
getphylo -l INFO
There are three levels currently used by getphylo: INFO, WARNING and DEBUG. WARNING will only print warning messages, INFO will print useful running information and DEBUG will print a debug information. INFO and WARNING are recommended. DEBUG is not recommended unless you need to submit a bug/error report.
getphylo can parallelise certain processes which will reduce runtime significantly. It does not do this by default and requires the use of multiple CPUs. You can set the number of CPUs with -c.
getphylo -c 8
getphylo doesn't use positional arguments so you can put the parameters together in any order.
getphylo -g 'input/*.myfiles.gb' -o ~/custom_directory/output_1 -c 8 -l INFO
Good luck and happy tree building!