Special operators

These are statements, operators, and expressions that are unique to bds. We just enumerate them here, but we explain details on what they mean and how they work in the following sections. This list is intended as a reference for people that are already familiar with these concepts, so don't despair if you don't understand what they mean.

Dependency operator

Dependency operator <- is true if any left-hand side file needs to be updated with respect to any right-hand side file

# Evaluate dependency 
if( 'out.txt' <- 'in.txt' )    print("File out.txt needs to be updated\n")

checkpoint

Create a checkpoint. Optional expression is a file name

# Wait for all tasks to finish
checkpoint "program.chp"

dep

Define dependency tasks. Tasks are not scheduled for execution until goal decides which dependencies must be executed to satisfy an output.

# Execute bwa command (create an index of the human genome)
task bwa index hg19.fasta

par

Execute code in parallel

par {
    for( int i=0 ; i < 10 ; i++ ) {
        print("This is executed in parallel: $i\n")
    }
}

                or just call a function in parallel

par doSomething(arg1, arg2)

sys

Execute an OS command. Execution is immediate and local (i.e. in the same computer as bds is running). It's intended for executing fast OS commands (not heavyweight processing).

# Execute an "ls" command
sys ls -al

task

Schedule an OS command for execution. Depending on the value of system, the execution can be local, in a cluster, remote server, etc.

# Execute bwa command (create an index of the human genome)
task bwa index hg19.fasta

wait

Wait for task(s) to finish. It can be one task, a list of tasks or all tasks (if no expression)

# Wait for all tasks to finish
wait

# Wait for one task to finish
wait taskId

# Wait for several tasks to finish
wait listOfTaskIDs