bioinformatics banner

Porting tomato analyses to pysano

Pysano is very similar to its predecessor, tomato, but there are a few differences.

Job directories

Your job directories can be in any location on the HCI servers visible to the pysano software. At present this includes the /home, /scratch, and /tomato file systems.

Starting and stopping jobs

To start a job in pysano, use the "pstart job_directory" command, where job_directory is the partial or full-path name of your job directory. For example, if your current directory is the job directory, you can use the command "pstart .". You can also start multiple jobs at the same time: pstart job_directory_1 job_directory_2 ....

To stop a job, use the "pstop job_directory" command.

Dry run jobs

You can perform a "dry run" in pysano using the "pdryrun job_directory" command. This submits the job to pysano for validation, but pysano will not execute the job on the computer cluster.


Pysano cmd.txt files may include several directives to instruct pysano how to run your job. The only differences with tomato are these:

The #e email_address directive now accepts the following options: -a, -b, and -e, or combinations of these (e.g. -abe). This is described in the reference manual here.

The #l lab_name directive is no longer accepted. This was supported in an early version of tomato.

b, r, a, and d files

Pysano does not use the "b", "a", and "d" files to control jobs, and no longer creates the "r" file which indicates a job is running. It does create the same stdout.txt and stderr.txt files that tomato creates.