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PSOT usage
==========

PSOT comes along as the commandline tool `psot`. It has two subcommands::

  info    -> show information about available modules and profiles
  analyze -> runs a profile for a protein fasta file


Basic execution
---------------

::

  psot analyze -f myfasta.faa -o results -p fast


Live mode execution
-------------------

During live mode execution PSOT will output results for already finished
modules as soon they become ready into a subfolder `live` within the results
folder.

::

  psot analyze -f myfasta.faa -o results -p fast -l

Cluster mode
------------

PSOT can take leverage of your compute cluster. At the moment it only supports
SGE. To use the cluster set the `-C` option.

::

  psot analyze -f myfasta.faa -o results -p fast -l -C

Debug mode execution
--------------------

PSOT has a few options for debugging. You can specify the execution directory
for the generated nextflow script via `-e <path>` and output the configuration
state via `-d`. If `-e` and `-d` are both specified then the execution
directory will not be removed.

::
  
  psot analyze -f myfasta.faa -o results -p fast -l -C -e ~/my_exec_dir -d