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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
Code Block | ||
---|---|---|
| ||
$ 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.list
Code Block title List of Shrimp commands gmapper-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
.Code Block title Using launcher_creator.py launcher_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.
Code Block title qsub the new launcher qsub map_sample.sge