How to setup galaxy with TORQUE in Amazon's cloud

example_tool.py

#!/usr/bin/python

import sys

'''
Just a simple tool that adds the line number at
the end of each line
'''

with open(sys.argv[1]) as f_in, open(sys.argv[2], 'w') as f_out:
    c = 0
    for l in f_in:
        c += 1
        f_out.write(l.replace('\n', '') + '\t%i'%c + '\n')

example_tool.xml

<tool id="custom_tool_1" name="Custom Tool 1" version="0.1.0">
  <description>Experimental tool 1</description>
  <command interpreter="python">example_tool.py $input $output</command>
  <inputs>
    <param format="tabular" name="input" type="data" label="Source file"/>
  </inputs>
  <outputs>
    <data format="tabular" name="output" />
  </outputs>

  <tests>
    <test>
      <param name="input" value="test_input.txt"/>
      <output name="output" file="test_output.txt"/>
    </test>
  </tests>

  <help>
The best tool ever.
  </help>

</tool>

locations.md

The location of the files

• example_tool.py tools/mytools
• example_tool.xml tools/mytools
• my_tool_conf.xml config/
• my_job_conf.xml config/

my_job_conf.xml

<?xml version="1.0"?>
<!-- A sample job config that explicitly configures job running the way it is configured by default (if there is no explicit config). -->
<job_conf>
    <plugins>
        <plugin id="local" 
                type="runner"
                load="galaxy.jobs.runners.local:LocalJobRunner" 
                workers="4"/>
        <plugin id="torque1" type="runner" 
                load="galaxy.jobs.runners.pbs:PBSJobRunner" 
                workers="2"/>
    </plugins>
    <handlers>
        <handler id="main"/>
    </handlers>
    <destinations default="local">
        <destination id="local" runner="local"/>
        <destination id="torque1_dst" runner="torque1"/>
    </destinations>
    <tools>
        <tool id="custom_tool_1" destination="torque1_dst"/>
    </tools>
</job_conf>

my_tool_conf.xml

<section name="MyTools" id="mTools">
    <tool file="mytools/example_tool.xml" />
</section>

test_input.txt

a	b	c
e	f	g
h	i	j