Hi Lyad and John,

Thanks for your replies and sorry for my no detailed question.

Well, I'm developing a tool that is applied to analyse PDB files (proteomics stuffs) ,compare them, and create a ranking sort by the best solutions (PDB files), making some graphs and 3D images. This tool will have as output a HTML file with all these generated files. 

I would like to access and use the information about the job, like ID and metrics for example, and write on this HTML output file. So, to do that, I think, I need to be able to use the Galaxy lib, but I couldn't create objects using the available class, like JobWrapper. Maybe I'm looking to the wrong place to take these information.

Is it possible?

I hope I was more detailed.

Best regards,


2014-10-06 22:32 GMT-03:00 John Chilton <jmchilton@gmail.com>:
Yes - I am with Iyad - having more context would probably help :). You
can inject job_wrapper related stuff into tool execution in a very
round about way perhaps by creating a dynamic job destination that
consumes the job_wrapper and then creates a job destination with
enviornment variables set to whatever it is you job needs. But that
solution is not very portable or simple - I can try to walk through
the steps in more detail though if it would be useful.


On Mon, Oct 6, 2014 at 9:28 PM, Kandalaft, Iyad
<Iyad.Kandalaft@agr.gc.ca> wrote:
> Tell us what you are trying to do and maybe someone might know the way to solve it.  It could be easier, the same, or more difficult than you imagined.
> Iyad Kandalaft
> Bioinformatics Programmer
> Microbial Biodiversity Bioinformatics
> Science & Technology Branch
> Agriculture & Agri-Food Canada
> Iyad.Kandalaft@agr.gc.ca | (613) 759-1228
> ________________________________
> From: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] on behalf of Alexandre Defelicibus [adefelicibus@gmail.com]
> Sent: October 6, 2014 4:50 PM
> To: <galaxy-dev@bx.psu.edu>
> Subject: [galaxy-dev] Job wrapper object
> Hi all,
> I'm developing some tools on my Galaxy instance and I need to get some information about the job that a tool creates.
> The question is, how can I have a job_wrapper object in my tool wrapper? I tried to use the reserved variable $__app__, but I got errors.
> I couldn't import and use the galaxy lib in order to get the job information.
> Could someone show me the correct way to do that, with some examples?
> I appreciate all the help.
> Best regards,
> --
> Alexandre Defelicibus
> Mestrando em Bioengenharia
> Programa de Pós-Graduação em Bioengenharia
> Universidade de São Paulo - USP
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Alexandre Defelicibus
Mestrando em Bioengenharia
Programa de Pós-Graduação em Bioengenharia
Universidade de São Paulo - USP