9:31 p.m.
Sorry for the long delay on this. You can get access to the job id and
perhaps metric information of a previous job by doing
$input.dataset.creating_job
That will give the job model object and from there you can use
.metrics to fetch the metrics. I consider it breaking Galaxy
abstractions so be careful if you decide to use it - we may break that
at some point.
-John
On Tue, Oct 7, 2014 at 7:13 PM, Alexandre Defelicibus
<adefelicibus(a)gmail.com> wrote:
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 <jmchilton(a)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.Kandalaft(a)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(a)agr.gc.ca | (613) 759-1228
> > ________________________________
> > From: galaxy-dev-bounces(a)lists.bx.psu.edu
> > [galaxy-dev-bounces(a)lists.bx.psu.edu] on behalf of Alexandre Defelicibus
> > [adefelicibus(a)gmail.com]
> > Sent: October 6, 2014 4:50 PM
> > To: <galaxy-dev(a)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