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@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

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

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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@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@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@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

___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/

-- Alexandre Defelicibus Mestrando em Bioengenharia Programa de Pós-Graduação em Bioengenharia Universidade de São Paulo - USP