Configuring the BAM pipeline

The BAM pipeline supports a number of command-line options (see paleomix bam run --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/bam_pipeline.ini, such as:

max-threads = 16
bowtie2-max-threads = 1
bwa-max-threads = 1
jar-root = /home/username/install/jar_root
jre-option = -Xmx4g
log-level = warning
temp-root = /tmp/username/bam_pipeline

Options in the configuration file correspond directly to command-line options for the BAM 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 bam_pipeline.ini file. For example, if max-threads is set to 4 in the bam_pipeline.ini file, but the pipeline is run using paleomix bam run --max-threads 10, then the max threads value is set to 10.