1.3 Running ATLAS

1.3.1 Argument syntax

The program ATLAS is launched via the command line, followed by the task name and argument names and the name of argument input files.

/path/to/atlas/build/atlas [taskname] --[argument_name] /path/to/input/for/argument/[argument_input_file]

Or you can add the path to atlas as an alias in your .bashrc file as follows to avoid having to indicate the path to atlas/build all the time.

alias atlas='/path/to/atlas/build/atlas'

atlas [taskname] --[arguments] /path/to/input/for/argument/[argument_input_file]

On the command line, the first entry must be the exact task name (e.g. BAMDiagnostics), followed by the argument names and their optional values. The order of arguments does not matter and if the same argument is listed more than once, only the latest entry is considered (facilitates the use of default-parameters for your pipelines). Go to Quickstart for a usage example.

Specific parameters can be found on the respective page of this manual. A list of all tasks can be found here. Engine parameters that are common to all tasks can be found here.

1.3.2 Argument files

All necessary arguments can also be specified in the argument file. On each line, you can specify a pair of argument name and corresponding value (separated by one or several white space characters, i.e. blanks or tabs). The order is of no importance. Comments are proceeded with a double slash ’‘//’’. Empty lines may be present anywhere within the file and are ignored.

For example, if the argument file is named example.arguments, the program has to be launched as follows:

/path/to/atlas/build/atlas example.arguments

An example for a *.arguments file to run BAMDiagnostics would be:

task BAMDiagnostics
// this is a comment
bam example.bam
//comment
filterMappingLength [55,100]
keepDuplicates
filterSoftClips //add comment here
// Add additional arguments as required

Additional, arguments can be passed on the command line. In that case, they will be interpreted “after” the arguments from the file and overwrite double entries.

1.3.3 Progress Report & Log File

By default, ATLAS writes out verbose information to stdout. To reduce the amount of information printed, use the argument --silent. To save the progress report into a file (e.g. out.txt), simply redirect the output using /path/to/atlas/build/atlas example.arguments verbose > out.txt

Alternatively, ATLAS can also write the progress report to a log file. To invoke this, simply use the argument --logFile, followed by the name of the desired file. Note that this will overwrite any existing file with that name. Note, verbose and logFile can both be used at the same time.