All Seal tools can read properties from a Seal configuration file. This allows you to write the properties you normally use to a file and re-use them for all runs, thus favouring manageability and simplicity.
Default configuration file: $HOME/.sealrc
If a configuration file exists at the default location, the Seal tools will load it automatically.
You can override the default configuration filename with the option --seal-config. Thus, you can have multiple preset configurations. For instance,
seal seqal --seal-config rna-runs.cfg input output reference.tar seal seqal --seal-config full_sample_runs.cfg input output reference.tar
The configuration file format resembles very much the traditional Windows INI file format and the Python ConfigParser file format; the main difference is that the Seal configuration is case-sensitive. Here are the main points:
Here is an example:
# Before any section you can specify properties that will apply to all sections. # They go in the DEFAULT section. # You can also use this file to specify Hadoop configuration properties. mapred.compress.map.output=true [DEFAULT] # You can also explicitly specify the DEFAULT section [Prq] # this property will only be read by Prq seal.prq.min-bases-per-read = 40 [Seqal] # maybe you usually have sanger-encoded base qualities seal.seqal.fastq-subformat=fastq-sanger # you can also specify Hadoop configuration options specific to one # tool (seqal in this case). This property setting will override the default # setting above, but only for seqal. mapred.compress.map.output=false
When the same property is set in various places, the following precedence order is used to decide which one to use: