Seal Config File

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.

Note

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

Config File Format

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:

• A section starts with the syntax [SectionName]. All properties set in the lines following the section title will be part of the named section.
• Properties are set as in property_name = value or property_name: value.
• There is a “DEFAULT” section whose properties are inherited by all tools. Properties set before any section is declared also go into this section.
• Blank lines are ignored.
• Line comments start with # or ;
• Whitespace around property names and values is ignored.

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

Precedence

When the same property is set in various places, the following precedence order is used to decide which one to use:

1. Command line. Values set with -D on the command line have the highest precedence.
2. Tool’s own section in config file.
3. DEFAULT section in config file.
4. Default property values, if any.