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,
Alexandre
2014-10-06 22:32 GMT-03:00 John Chilton jmchil...@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.
-John
On Mon, Oct 6, 2014 at 9:28 PM, Kandalaft, Iyad
iyad.kandal...@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.kandal...@agr.gc.ca | (613) 759-1228
From: galaxy-dev-boun...@lists.bx.psu.edu [
galaxy-dev-boun...@lists.bx.psu.edu] on behalf of Alexandre Defelicibus [
adefelici...@gmail.com]
Sent: October 6, 2014 4:50 PM
To: galaxy-...@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
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