What Does It Do
launcher_creator.py is a convenience utility that automates creating a launcher for Lonestar based on parameters (and commands) you give it. It outputs a .sge file that can be submitted to Lonestar using qsub. It can run both Bash commands on a single node and/or a parametric list of commands to be dispatched to multiple nodes.
How To Use It
$ launcher_creator.py <options listed below> $ qsub <launcher file>
-n |
name |
The name of the job. |
-a |
allocation |
The allocation you want to charge the run to. |
-q |
queue |
The queue to submit to, like 'normal' or 'largemem', etc. |
-w |
wayness |
Optional The number of jobs in a job list you want to give to each node. (Default is 12.) |
-t |
time |
Time allotment for job, format must be hh:mm:ss. |
-e |
Optional Your email address if you want to receive an email from Lonestar when your job starts and ends. |
|
-H |
holding for job |
Optional The launcher will wait for the specified job to finish before launching this job. |
-l |
launcher |
Filename of the launcher. (Default is |
-m |
modules |
Optional String of module management commands. |
-b |
Bash commands |
Optional String of Bash commands to execute. |
-j |
Command list |
Optional Filename of list of commands to be distributed to nodes. |
Note that while the "-b" and "-j" options are both optional, using neither would pass no work to Lonestar, so you want to use at least one of them!
Examples
Distributing Shrimp to four nodes
- Make a list of the Shrimp commands to run. You can do this in a text editor, algorithmically with a Bash loop, whatever. Let's pretend this text is saved as
mapping_commands.listList of Shrimp commandsgmapper-ls -N 6 --qv-offset 33 -p opp-in --fastq -1 Sample_R1-00.fq -2 Sample_R2-00.fq reference.fasta > Sample_mapped-00.sam gmapper-ls -N 6 --qv-offset 33 -p opp-in --fastq -1 Sample_R1-01.fq -2 Sample_R2-01.fq reference.fasta > Sample_mapped-01.sam gmapper-ls -N 6 --qv-offset 33 -p opp-in --fastq -1 Sample_R1-02.fq -2 Sample_R2-02.fq reference.fasta > Sample_mapped-02.sam gmapper-ls -N 6 --qv-offset 33 -p opp-in --fastq -1 Sample_R1-03.fq -2 Sample_R2-03.fq reference.fasta > Sample_mapped-03.sam
- Generate a launcher using
launcher_creator.py.Using launcher_creator.pylauncher_creator.py -q normal -a MyAllocation -n MapSample -j mapping_commands.list -w 2 -t 6:00:00 -l map_sample.sge -m "module load shrimp"
- Submit the newly-created launcher.
qsub the new launcher
qsub map_sample.sge
