Thank You Danno,

I will give it a try.  By the way, is there a way to run a workflow and create a new history every time new data sets (fastq) is available programmatically?  I have looked at the scripts at the ~api/ (ie. Example_watch, workflow_excute) scripts but I do not think these scripts can create a new history every time they get executed unless I am totally off.

Regards

From: Dannon Baker [mailto:dannon.baker@gmail.com]
Sent: Tuesday, April 30, 2013 2:48 PM
To: Hakeem Almabrazi
Cc: galaxy-dev@lists.bx.psu.edu List
Subject: Re: [galaxy-dev] print out workflow execution commands!

You'll want the job table, and the field is command_line.

On Tue, Apr 30, 2013 at 3:26 PM, Hakeem Almabrazi <halmabrazi@idtdna.com> wrote:

Yes, I am actually looking for the actual command lines that were executed.  I would like to know exactly how these tools are called so I can mimic that process from outside Galaxy env. I guess I have to dig into the database, but can you tell me what table(s) should I be looking at to find out that info?

From: Dannon Baker [mailto:dannon.baker@gmail.com]
Sent: Tuesday, April 30, 2013 2:11 PM
To: Hakeem Almabrazi
Cc: galaxy-dev@lists.bx.psu.edu List
Subject: Re: [galaxy-dev] print out workflow execution commands!

Hi Hak,

Yes, you can get all of the information saved for a particular workflow - in the abstract, not a particular workflow execution - by going to 'Download or Export' in the workflow menu, then click "Download to File".  This will give you a .ga file which contains the steps in JSON format, which is fairly human readable.

If you're asking for the actual command lines executed, you'll have to dig in the database a little bit to find the exact jobs you've executed and grab the command line from there, as this information isn't tied to the workflow itself -- at least, not directly.

-Dannon

On Tue, Apr 30, 2013 at 3:05 PM, Hakeem Almabrazi <halmabrazi@idtdna.com> wrote:

Hi everyone,

Is there an easy way to view/save/print out the executed commands and their parameters for a workflow?   I want to see what is going on for certain steps in my workflow.

Regards,

Hak

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