Configuring the phylogenetic pipelineΒΆ
The Phylo pipeline supports a number of command-line options (see paleomix phylo --help
). These options may be set directly on the command-line (e.g. using --max-threads 16
), but it is also possible to set default values for such options.
This is accomplished by writing options in ~/.paleomix/phylo_pipeline.ini
:
max-threads = 16
examl-max-threads = 7
log-level = warning
temp-root = /tmp/username/phylo_pipeline
Options in the configuration file correspond directly to command-line options for the Phylo pipeline, with leading dashes removed. For example, the command-line option --max-threads
becomes max-threads
in the configuration file.
Options specified on the command-line take precedence over those in the phylo_pipeline.ini
file. For example, if max-threads
is set to 4 in the phylo_pipeline.ini
file, but the pipeline is run using paleomix phylo --max-threads 10
, then the max threads value is set to 10.