Re: [galaxy-dev] list of names, variables that cannot be used inside XML

[Katherine Beaulieu]

This is the page describing the xml syntax that can be used to wrap tools.
If its not on this page I would guess that you can't use it in your xml
code.
https://docs.galaxyproject.org/en/latest/dev/schema.html

On Mon, Feb 20, 2017 at 5:22 AM, Jochen Bick 
wrote:

> Hi all,
>
> is there any list available of names that are not allowed to use inside
> xml code? I just found out that "pmode" is one of them.
>
> Cheers Jochen
>
>
> --
> ETH Zurich
> *Jochen Bick*
> Animal Physiology
> Institute of Agricultural Sciences
> Postal address: Universitätstrasse 2 / LFW B 58.1
> Office: Tannenstrasse 1 / TAN D 6.2
> 8092 Zurich, Switzerland
>
> Phone +41 44 632 28 25
> jochen.b...@usys.ethz.ch 
> www.ap.ethz.ch
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Re: [galaxy-dev] Check running jobs

[Katherine Beaulieu]

I think this is a bit more complicated than what I am looking for. All I am
looking for is a way to get the result of this query:

> jobs = trans.sa_session.query( trans.app.model.Job ) \
>.filter( and_(
> trans.app.model.Job.table.c.update_time < cutoff_time,
>   or_(
> trans.app.model.Job.state == trans.app.model.Job.states.NEW,
>
> trans.app.model.Job.state == trans.app.model.Job.states.QUEUED,
>
> trans.app.model.Job.state == trans.app.model.Job.states.RUNNING,
>
> trans.app.model.Job.state == trans.app.model.Job.states.UPLOAD ) ) ) \
>.order_by(
> trans.app.model.Job.table.c.update_time.desc() ).all()

from the file /lib/galaxy/web/base/controllers/admin.py, without having to
use the UI. Has anyone done something like this before?

On Fri, Jan 27, 2017 at 10:03 AM, Peter Cock <p.j.a.c...@googlemail.com>
wrote:

> Ah - I assumed you meant from the user-facing UI, or the reports page.
>
> I would suggest exploring the advance job metrics options, see e.g.
>
> https://github.com/galaxyproject/galaxy/blob/dev/
> config/job_metrics_conf.xml.sample
>
> I've never used it, but perhaps the backend using Collectl
> (http://collectl.sourceforge.net/) would cover this?
>
> Peter
>
> On Fri, Jan 27, 2017 at 2:50 PM, Katherine Beaulieu
> <katherine.beaulieu...@gmail.com> wrote:
> > Ok so there is no way to access the galaxy object outside of galaxy? I'm
> > looking for something like the 'trans' variable often seen throughout the
> > Galaxy code base so that I can use sqlalchemy and make a database query.
> > Thanks for replying.
> > Katherine
>
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Re: [galaxy-dev] Check running jobs

[Katherine Beaulieu]

Ok so there is no way to access the galaxy object outside of galaxy? I'm
looking for something like the 'trans' variable often seen throughout the
Galaxy code base so that I can use sqlalchemy and make a database query.
Thanks for replying.
Katherine

On Fri, Jan 27, 2017 at 5:40 AM, Peter Cock <p.j.a.c...@googlemail.com>
wrote:

> Hi Katherine,
>
> I don't think Galaxy itself will tell you this, in part because the
> details would be dependent on the Cluster being used.
>
> I would do that via whatever cluster management system you are running
> (e.g. qstat or qmon if using SGE).
>
> By default all the jobs will be submitted by the Galaxy user account,
> but if you are submitting jobs as the individual users then you can
> still spot Galaxy jobs via their naming convention (starting "g",
> number, underscore, ..., tool name, user's email).
>
> Peter
>
> On Thu, Jan 26, 2017 at 6:58 PM, Katherine Beaulieu
> <katherine.beaulieu...@gmail.com> wrote:
> > Hi there,
> > We are trying to build our own Galaxy cluster and I was wondering if
> there
> > was a way to check if there are any running Galaxy jobs on a specific
> > server? This would be to determine whether or not to remove the server
> from
> > the cluster.
> > Thanks!
> > Katherine
> >
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[galaxy-dev] Check running jobs

[Katherine Beaulieu]

Hi there,
We are trying to build our own Galaxy cluster and I was wondering if there
was a way to check if there are any running Galaxy jobs on a specific
server? This would be to determine whether or not to remove the server from
the cluster.
Thanks!
Katherine
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[galaxy-dev] Code File Execution

[Katherine Beaulieu]

Hi Everyone,
Does anyone know how execution of code files happens? Is there a function
somewhere that fills the parameters in?
Cheers,
Katherine
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Re: [galaxy-dev] Galaxy on the Cloud with Openstack

[Katherine Beaulieu]

Hi Enis,
Yes I did go through this process and got stuck at running the images.yml
file. I wasn't able to run with packer so am trying it without it. Here is
the error I got stopped at:

TASK [smola.java : Install Java packages]
**

Monday 14 November 2016  17:27:15 + (0:00:00.552)   0:00:01.830
***

failed: [localhost] (item=[u'java_packages']) => {"failed": true, "item":
["java_packages"], "msg": "No package matching 'java_packages' is
available"}

to retry, use: --limit @/home/ubuntu/galaxy-cloudman-playbook/image.retry


Do you have an idea of what could be the cause of this error?

Thanks for the help!

On Mon, Nov 14, 2016 at 11:58 AM, Enis Afgan <enis.af...@irb.hr> wrote:

> Hi Katherine,
> A good starting point is the official documentation available here
> https://wiki.galaxyproject.org/CloudMan/Building. It links to a few more
> technical README's from there. Did you go through this? Were there issues
> you encountered?
> Overall, the complete deployment is a reasonably involved process that is
> somewhat dependent on the infrastructure internals so it'll take some time
> and understanding of the process to get it done. Feel free to email with
> any questions.
>
>
>
> On Tue, Nov 8, 2016 at 1:31 PM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
>> Hi Galaxy Community,
>> Does anyone have a really great guide as to how I could get Galaxy on the
>> Cloud up and running with our private openstack cloud orchestrated by fuel
>> 7.0?
>> Cheers,
>> Katherine
>>
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[galaxy-dev] Fwd: Workflow Execution Files

[Katherine Beaulieu]

-- Forwarded message --
From: Katherine Beaulieu <katherine.beaulieu...@gmail.com>
Date: Mon, Oct 24, 2016 at 2:55 PM
Subject: Re: [galaxy-dev] Workflow Execution Files
To: Aysam Guerler <aysam.guer...@gmail.com>


Awesome thanks Aysam! I was wondering if you know what happens to the job
parameters once they go through 'POST'? I am trying to add my own parameter
which should show up in the database. I was successful for an individual
job in tool-form.js, by just adding an attribute to the job_def.inputs
parameter but in tool-form-composite.js, just adding a parameter to
job_def.parameters[step size][job_input_id] doesn't automatically add to
the database.
Thanks for the help!

On Mon, Oct 24, 2016 at 9:57 AM, Aysam Guerler <aysam.guer...@gmail.com>
wrote:

> Hi Katherine,
>
> The tool form is build and submitted to the API through
> tool-form-composite.js.
>
> Sam
>
> On Mon, Oct 24, 2016 at 9:29 AM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
>> Hi Everyone,
>> Does anyone know what files workflow execution goes through? I had
>> assumed it just went through the same files as individual jobs for each
>> step but I don't think that's the case. I was looking at tool-form.js but
>> it doesn't seem to be executing that file.
>> Thanks!
>> Katherine
>>
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>
>
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[galaxy-dev] Workflow Execution Files

[Katherine Beaulieu]

Hi Everyone,
Does anyone know what files workflow execution goes through? I had assumed
it just went through the same files as individual jobs for each step but I
don't think that's the case. I was looking at tool-form.js but it doesn't
seem to be executing that file.
Thanks!
Katherine
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Re: [galaxy-dev] Storing data in the user session

[Katherine Beaulieu]

Hi Steve,
In terms of accessing the user's api key within a tool definition file,
have a look at this thread I had started. John had suggested something but
I haven't gotten it to work but maybe you will have more luck than me.
http://dev.list.galaxyproject.org/Workflow-ID-Galaxy-Instance-URL-API-Key-in-Galaxy-Tool-Config-td4669906.html#a4670104
Cheers,
Katherine

On Mon, Oct 17, 2016 at 5:17 PM, Steve Cassidy 
wrote:

> Hi Bjoern,
>  just wanting to revisit this question and perhaps get an update on what
> you were doing for extending the user profile.
>
> I just noticed in the galaxy sources the option to add ‘forms’ to be
> filled out at registration time. The admin interface seems to allow me to
> create  a form but it doesn’t appear when I try to register.  The code for
> this seems to be 2-5 years old so perhaps it’s a forgotten corner?
>
> https://github.com/galaxyproject/galaxy/tree/dev/templates/admin/forms
>
> Anyway, if you have made any progress on this I’d be happy to hear about
> it.  I’d like to be able to store the user’s API key in the profile and
> access it from a tool definition file.
>
> Cheers,
>
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
> On 28 Jul. 2016, at 2:59 pm, Björn Grüning 
> wrote:
>
> Hi Steve & Mohammed,
>
> I'm working on a user-profile extension to get credentials for a user,
> but this will take a few more weeks sorry.
>
> In the meantime can you look at the following idea:
>
> my_programm.py --credentials $USER_CREDENTIALS --arguments
>
> The variable $USER_CREDENTIALS is set during job execution with dynamic
> destination mappings
> https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_
> Destination_Mapping
>
> What do you think, would this work for you?
> This assumes you as admin can pass along the user credentials if you
> know the username.
>
> If not please get in touch and I will tell you about my plans to extend
> the user-preferences maybe you can help me with this to speed things up.
>
> Ciao,
> Bjoern
>
>
> Hi Bjorn,
> sure, I don’t want to have the credentials stored in the tool but the tool
> needs to act on behalf of the user to retrieve data from the repository, so
> it needs access to credentials.  This could for example be a token
> generated
> via an OAuth2 exchange - basically something that is sent along with every
> http request to the remote resource to authenticate the user.
>
> My thought is that this could be stored in the user profile if this can be
> made
> available to the tool in the same way that __user_email__ is now.
>
> When you say ‘on the framework level’ do you mean by Galaxy?
>
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
> On 28 Jul 2016, at 5:23 PM, Björn Grüning 
> wrote:
>
> Hi Steve,
>
> can you explain the larger use-case behind it. Imho you should not
> populate a tool with credentials, this should be handled on the
> framework level.
>
> Hope you are fine,
> Bjoern
>
> Am 28.07.2016 um 03:15 schrieb Steve Cassidy:
>
> Hi again,
>  I’m looking for the right way to store some user credentials in the
> galaxy session so that tools can work on behalf of the user with our
> repository.
>
> Currently users have an API key and they need to upload it as a data
> item to that is then passed to each tool that needs it as input.  This
> doesn’t seem like the right solution since the API key becomes part of
> the history and so would be shared if the history were shared.
>
> What would be better would be a way of storing the API key in the user
> session and then being able to pass that into a tool.
>
> I note that there are a few user session variables available in the tool
> xml file: __user__, __user_email__, __user_name__ and __user_id__.
> There is also a user preferences page where they can fill out a few
> details.  However, I can’t see a mechanism to extend this in any way and
> have extra properties in the preferences pane that would then be
> available to tools via the template file.
>
> I can see that the standard practice for the data sources on
> usegalaxy.org  is to send the user off to a
> repository website to find data that is then posted back to the galaxy
> server.  This isn’t appropriate for us since the interaction with the
> repository is not just for downloading a single dataset - tools will
> query the repository, download various kinds of data and possibly upload
> new data, so we need to store user credentials in some way.
>
> Is there already a good way to achieve this or is this an enhancement to
> Galaxy?
>
> Thanks,
>
> Steve
>
>
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
> 
>
>
>
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[galaxy-dev] Job_id in a galaxy tool

[Katherine Beaulieu]

Hello Galaxy Community,
Is it possible to get the job_id listed on the info 'eye' page within a
tool wrapper?
Katherine
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Re: [galaxy-dev] Modifying Values in the Database

[Katherine Beaulieu]

Hi John, I ended up reading about using sqlalchemy, thanks for getting back
to me though!

On Fri, Sep 30, 2016 at 8:57 AM, John Chilton <jmchil...@gmail.com> wrote:

> Is this something inside the application or external to it? If it is
> external to the application - I'd probably just target the database
> directly (Postgres or MySQL). The internals of Galaxy use sqlalchemy
> for the most part (http://www.sqlalchemy.org/). I've done a lot with
> the database but I've never really read a tutorial on sqlalchemy - I
> just find something close in the code and hack on that pattern.
>
> The are a lot of examples in the code of using sqlalchemy - if you
> want an example of like using postgres directly - here is one:
>
> https://github.com/galaxyproject/galaxy/blob/dev/scripts/cleanup_datasets/
> pgcleanup.py
>
> -John
>
> On Tue, Sep 6, 2016 at 9:13 AM, Katherine Beaulieu
> <katherine.beaulieu...@gmail.com> wrote:
> > Hello Everyone,
> > I am trying to create a query to modify a value from a table in the
> galaxy
> > database, but don't quite know what this language is that is being used
> to
> > modify the database. The only command I know of are sa_session.add and
> > sa_session.flush. Any help would be really appreciated!
> > Katherine
> >
> > ___
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Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

[Katherine Beaulieu]

If anyone was wondering, I ended up sending the name of the repeat to the
function in the code file which is a list of dictionaries and in the
dictionaries you have an index and the other parameters in the repeat so as
long as you know the name of the parameters you are golden.

On Fri, Sep 2, 2016 at 9:07 PM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

>
>
> On Fri, Sep 2, 2016 at 9:07 PM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
>> Hi Bjorn,
>> Thank you for taking the time to reply to my question. I don't think this
>> quite fits what I am trying to accomplish. I am trying to pass a set of
>> metadata key value pairs, where the user can have as many key value pairs
>> as they want, generated with a repeat parameter. I would need to pass the
>> entire contents of the repeat parameter to the code file to generate a
>> dynamic select list. Do you think this is possible? Perhaps I misread the
>> file you have sent me a link to.
>> Thanks,
>> Katherine
>>
>> On Fri, Sep 2, 2016 at 6:12 PM, Björn Grüning <bjoern.gruen...@gmail.com>
>> wrote:
>>
>>> Hi Katherine,
>>>
>>> have a look at this one using repeats:
>>>
>>> https://github.com/bgruening/galaxytools/blob/master/tools/d
>>> eseq2/deseq_helper.py
>>>
>>> Ciao,
>>> Bjoern
>>>
>>>
>>> Am 01.09.2016 um 13:58 schrieb Katherine Beaulieu:
>>> > Hello Galaxy Community,
>>> > I was wondering if anyone had ever come across a situation where they
>>> > have had to pass the contents of a repeat parameter to a code file in a
>>> > Galaxy tool config? Is there any way to do this?
>>> > Katherine
>>> >
>>> >
>>> > ___
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>>> > in your mail client.  To manage your subscriptions to this
>>> > and other Galaxy lists, please use the interface at:
>>> >   https://lists.galaxyproject.org/
>>> >
>>> > To search Galaxy mailing lists use the unified search at:
>>> >   http://galaxyproject.org/search/mailinglists/
>>> >
>>>
>>
>>
>
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[galaxy-dev] How to set up handler and web server process within a virtual machine

[Katherine Beaulieu]

Hi Everyone,
I am looking to set up a web server and handler process for galaxy within a
virtual machine. I've tried following the instructions written here:
https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling#Starting_and_Stopping
But, I can still start Galaxy with sh run.sh, also the commands associated
with supervisord don't seem to work, I keep getting this error: "Error:
positional arguments are not supported:"

Lastly, how can I confirm that this is working? Will I see two 'python'
processes running when I run top?

Katherine
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Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

[Katherine Beaulieu]

On Fri, Sep 2, 2016 at 9:07 PM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hi Bjorn,
> Thank you for taking the time to reply to my question. I don't think this
> quite fits what I am trying to accomplish. I am trying to pass a set of
> metadata key value pairs, where the user can have as many key value pairs
> as they want, generated with a repeat parameter. I would need to pass the
> entire contents of the repeat parameter to the code file to generate a
> dynamic select list. Do you think this is possible? Perhaps I misread the
> file you have sent me a link to.
> Thanks,
> Katherine
>
> On Fri, Sep 2, 2016 at 6:12 PM, Björn Grüning <bjoern.gruen...@gmail.com>
> wrote:
>
>> Hi Katherine,
>>
>> have a look at this one using repeats:
>>
>> https://github.com/bgruening/galaxytools/blob/master/tools/d
>> eseq2/deseq_helper.py
>>
>> Ciao,
>> Bjoern
>>
>>
>> Am 01.09.2016 um 13:58 schrieb Katherine Beaulieu:
>> > Hello Galaxy Community,
>> > I was wondering if anyone had ever come across a situation where they
>> > have had to pass the contents of a repeat parameter to a code file in a
>> > Galaxy tool config? Is there any way to do this?
>> > Katherine
>> >
>> >
>> > ___
>> > 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:
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>> >
>> > To search Galaxy mailing lists use the unified search at:
>> >   http://galaxyproject.org/search/mailinglists/
>> >
>>
>
>
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Re: [galaxy-dev] Send repeat parameter to code file for multiple select list

[Katherine Beaulieu]

On Thu, Sep 1, 2016 at 9:36 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hi Peter,
> The code file tag is generally used in populating select lists. So
> basically you have a function from a code file that is loaded before
> runtime of the tool and you can dynamically load content based on that
> function and you can pass it parameters from your tool but I'm wondering
> how you would pass it the contents of a repeat parameter.
> This is how the code file tag works:
> https://wiki.galaxyproject.org/Admin/Tools/Custom%20Code
> Thanks,
> Katherine
>
> On Thu, Sep 1, 2016 at 8:23 AM, Peter Cock <p.j.a.c...@googlemail.com>
> wrote:
>
>> I'm not quite sure what you mean by a "code file", but if you
>> mean using the  tag, here's an example:
>>
>> https://github.com/peterjc/galaxy_mira/blob/master/tools/mir
>> a4_0/mira4_de_novo.xml
>>
>> I am using a Cheetah syntax for loop to access each entry
>> in a repeat parameter.
>>
>> Peter
>>
>> On Thu, Sep 1, 2016 at 12:58 PM, Katherine Beaulieu
>> <katherine.beaulieu...@gmail.com> wrote:
>> > Hello Galaxy Community,
>> > I was wondering if anyone had ever come across a situation where they
>> have
>> > had to pass the contents of a repeat parameter to a code file in a
>> Galaxy
>> > tool config? Is there any way to do this?
>> > Katherine
>> >
>> > ___
>> > 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:
>> >   https://lists.galaxyproject.org/
>> >
>> > To search Galaxy mailing lists use the unified search at:
>> >   http://galaxyproject.org/search/mailinglists/
>>
>
>
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[galaxy-dev] Send repeat parameter to code file for multiple select list

[Katherine Beaulieu]

Hello Galaxy Community,
I was wondering if anyone had ever come across a situation where they have
had to pass the contents of a repeat parameter to a code file in a Galaxy
tool config? Is there any way to do this?
Katherine
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[galaxy-dev] Batch Mode Tool Execution

[Katherine Beaulieu]

Hi Galaxy Community,
Does anyone know if it is possible to run a tool in batch mode if there is
no data type parameter in the tool? I'd love to be able to run a tool in
batch mode based on a multiple select list instead.
Katherine
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Re: [galaxy-dev] Parameters out

[Katherine Beaulieu]

Hi Devon,
Thanks for the information! Do you know where in the code base Galaxy
accesses these values for tool execution though?
Cheers,
Katherine

On Tue, Aug 30, 2016 at 8:44 AM, Devon Ryan <dpr...@dpryan.com> wrote:

> Hi Katherine,
>
> Check the 'job_parameter' table, though you'll need to find the
> correct job ID from the 'job' table.
>
> Devon
> --
> Devon Ryan, Ph.D.
> Email: dpr...@dpryan.com
> Data Manager/Bioinformatician
> Max Planck Institute of Immunobiology and Epigenetics
> Stübeweg 51
> 79108 Freiburg
> Germany
>
>
> On Tue, Aug 30, 2016 at 2:35 PM, Katherine Beaulieu
> <katherine.beaulieu...@gmail.com> wrote:
> > Hi everyone,
> > Does anyone know where parameters are being retrieved from the database
> > during tool execution within Galaxy's files. I am trying to change a
> value
> > in the database after the value has been retrieved.
> > Thanks!
> > Katherine
> >
> > ___
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[galaxy-dev] Parameters out

[Katherine Beaulieu]

Hi everyone,
Does anyone know where parameters are being retrieved from the database
during tool execution within Galaxy's files. I am trying to change a value
in the database after the value has been retrieved.
Thanks!
Katherine
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Re: [galaxy-dev] Workflow Compatibility

[Katherine Beaulieu]

Hi Brad,
So with multiple selection dropdown lists this is possible? Do you have an
example of a tool that can do this? Would it be possible to see an example
of the tools you are talking about? Thanks for the help!
Katherine

On Fri, Aug 26, 2016 at 12:05 PM, Langhorst, Brad <langho...@neb.com> wrote:

> Hi Katherine:
>
> I’d recommend not having users type in paths if at all possible (they will
> make frustrating mistakes).
> If there is a selection of these maybe consider turining them into
> dropdown lists.
>
> Either way,  these would be no different than e.g. user specified
> downsampling  amounts. or library names, etc.
> I have tools that accept many of these.
>
>
> Brad
>
> —
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
>
>
>
> On Aug 26, 2016, at 10:57 AM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
> What if its multiple file paths that the user types in rather than actual
> files, which makes it so the tool can't be executed in batch mode, would it
> still be workflow compatible at that point? Thanks for pointing me to the
> Bowtie wrappers as an example.
>
>
>
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Re: [galaxy-dev] Workflow Compatibility

[Katherine Beaulieu]

Hi Brad,
What if its multiple file paths that the user types in rather than actual
files, which makes it so the tool can't be executed in batch mode, would it
still be workflow compatible at that point? Thanks for pointing me to the
Bowtie wrappers as an example.
Katherine

On Fri, Aug 26, 2016 at 10:45 AM, Langhorst, Brad <langho...@neb.com> wrote:

> HI Katherine:
>
> Multi-input/output should work fine…
>
> You could have a look at the bowtie wrappers for an example.
>
> It takes up to 2 fastq files and a reference. I can output a few files
> (unmapped, mapped, etc)
>
>
> Brad
> —
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
>
>
>
> On Aug 26, 2016, at 10:42 AM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
>
>
> On Fri, Aug 26, 2016 at 10:42 AM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
>> Hi Peter,
>> I think I did not explain myself well. I meant that if I have a tool that
>> takes multiple file paths and outputs multiple Galaxy datasets to the
>> history, would this tool be workflow compatible, meaning capable of being a
>> part of any workflow? From the behaviour I am getting now I am assuming it
>> isn't but I just wanted to confirm that this isn't supported functionality.
>>
>> On Fri, Aug 26, 2016 at 10:34 AM, Peter Cock <p.j.a.c...@googlemail.com>
>> wrote:
>>
>>> Hi Katherine,
>>>
>>> Are you asking about compatibility staying on the same Galaxy
>>> instance, or the harder problem of compatibility sharing workflows
>>> between Galaxy servers?
>>>
>>> Taking data from input Galaxy datasets should be fine, anything else
>>> may not be portable. Even the relatively simple case of using
>>> datafiles referenced via an example.loc file (e.g. BLAST databases)
>>> would require the entries in the example.loc file be synchronised
>>> between Galaxy instances, and the associated data files too.
>>>
>>> Peter
>>>
>>>
>>> On Fri, Aug 26, 2016 at 1:27 PM, Katherine Beaulieu
>>> <katherine.beaulieu...@gmail.com> wrote:
>>> > Hi Everyone,
>>> > Would anyone be able to tell me the conditions which would make a tool
>>> > non-workflow compatible? I have a tool that imports files from a third
>>> party
>>> > application and auto-detects the file format. There is also the option
>>> to
>>> > upload multiple files at once so the tool always uploads at least two
>>> files.
>>> > From what I have described can anyone see why this tool would not be
>>> able to
>>> > send one of its files to the next tool in the chain, ex. a text
>>> manipulation
>>> > tool?
>>> > Thanks,
>>> > Katherine
>>> >
>>> > ___
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>>> >   http://galaxyproject.org/search/mailinglists/
>>>
>>
>>
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Re: [galaxy-dev] Workflow Compatibility

[Katherine Beaulieu]

On Fri, Aug 26, 2016 at 10:42 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hi Peter,
> I think I did not explain myself well. I meant that if I have a tool that
> takes multiple file paths and outputs multiple Galaxy datasets to the
> history, would this tool be workflow compatible, meaning capable of being a
> part of any workflow? From the behaviour I am getting now I am assuming it
> isn't but I just wanted to confirm that this isn't supported functionality.
>
> On Fri, Aug 26, 2016 at 10:34 AM, Peter Cock <p.j.a.c...@googlemail.com>
> wrote:
>
>> Hi Katherine,
>>
>> Are you asking about compatibility staying on the same Galaxy
>> instance, or the harder problem of compatibility sharing workflows
>> between Galaxy servers?
>>
>> Taking data from input Galaxy datasets should be fine, anything else
>> may not be portable. Even the relatively simple case of using
>> datafiles referenced via an example.loc file (e.g. BLAST databases)
>> would require the entries in the example.loc file be synchronised
>> between Galaxy instances, and the associated data files too.
>>
>> Peter
>>
>>
>> On Fri, Aug 26, 2016 at 1:27 PM, Katherine Beaulieu
>> <katherine.beaulieu...@gmail.com> wrote:
>> > Hi Everyone,
>> > Would anyone be able to tell me the conditions which would make a tool
>> > non-workflow compatible? I have a tool that imports files from a third
>> party
>> > application and auto-detects the file format. There is also the option
>> to
>> > upload multiple files at once so the tool always uploads at least two
>> files.
>> > From what I have described can anyone see why this tool would not be
>> able to
>> > send one of its files to the next tool in the chain, ex. a text
>> manipulation
>> > tool?
>> > Thanks,
>> > Katherine
>> >
>> > ___
>> > Please keep all replies on the list by using "reply all"
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>> >
>> > To search Galaxy mailing lists use the unified search at:
>> >   http://galaxyproject.org/search/mailinglists/
>>
>
>
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[galaxy-dev] Workflow Compatibility

[Katherine Beaulieu]

Hi Everyone,
Would anyone be able to tell me the conditions which would make a tool
non-workflow compatible? I have a tool that imports files from a third
party application and auto-detects the file format. There is also the
option to upload multiple files at once so the tool always uploads at least
two files. From what I have described can anyone see why this tool would
not be able to send one of its files to the next tool in the chain, ex. a
text manipulation tool?
Thanks,
Katherine
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Re: [galaxy-dev] Parameter Storing in Database

[Katherine Beaulieu]

On Thu, Aug 25, 2016 at 2:25 PM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hi Peter,
> No actually I meant in what file is the table job_parameter getting filled
> during execution?
> Katherine
>
> On Fri, Aug 5, 2016 at 3:00 PM, Peter van Heusden <p...@sanbi.ac.za> wrote:
>
>> You mean the stuff for the tool-data tables? As I understand it, it is
>> loaded in:
>>
>> lib/galaxy/tools/data/__init__.py
>>
>> There's a ToolDataTableManager and a TabularToolDataTable (with
>> associated TabularToolDataField).
>>
>> Peter
>>
>> On Fri, 5 Aug 2016 at 20:46 Katherine Beaulieu <
>> katherine.beaulieu...@gmail.com> wrote:
>>
>>> Would anyone be able to tell me in what file the storing of tool
>>> parameters into the database occurs?
>>> Thanks!
>>> Katherine
>>> ___
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>>
>>
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>>
>
>
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[galaxy-dev] Workflow ID, Galaxy Instance URL, API Key in Galaxy Tool Config

[Katherine Beaulieu]

Hi everyone,
We are trying to obtain the three things in the tile of this post to enable
a tool to use the bioblend api and get the .ga file so that any user can go
back into our system, get the workflow associated with the end file, get
the input parameters which are tags associated with the end file, and rerun
that workflow if necessary. So simply put I am asking if there is a way to
access a galaxy instance through the bioblend api from within a tool's
config xml file.

I have asked about getting the .ga file beforehand but still have not
solved this problem so if anyone has any experience with this please let me
know.
Cheers,
Katherine
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[galaxy-dev] Parameter Storing in Database

[Katherine Beaulieu]

Would anyone be able to tell me in what file the storing of tool parameters
into the database occurs?
Thanks!
Katherine
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[galaxy-dev] Galaxy URL and api key tool config

[Katherine Beaulieu]

Hi everyone,
I was wondering if anyone knew how to pass the url of your galaxy instance
to a tool as well as a way to authenticate so I could use the bioblend api
within my tool?
Thanks,
Katherine
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Re: [galaxy-dev] Deprecated code file tag

[Katherine Beaulieu]

On Wed, Aug 3, 2016 at 11:36 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Ok thanks for the information!
>
> On Wed, Aug 3, 2016 at 11:21 AM, Eric Rasche <e...@tamu.edu> wrote:
>
>> Hi Katherine,
>>
>> There is unfortunately no direct replacement to code files (but I hear it
>> might still work...if you have internal-only tools, that might be an
>> option). I have the exact same use case as you but do not have a clean
>> Galaxy solution to offer. I've opened an issue on github
>> <https://github.com/galaxyproject/galaxy/issues/2712> for this.
>>
>> Cheers,
>> Eric
>>
>>
>> On 03. aug. 2016 12:35, Katherine Beaulieu wrote:
>>
>> Hi everyone,
>> I can't remember where I came across this but I read somewhere that the
>> > it was being replaced with? I use it to get a list of items from a remote
>> service to display in a select list for two of my tools.
>> Thanks!
>> Katherine
>>
>>
>> ___
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>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>> --
>> Eric Rasche
>> Programmer II
>>
>> Center for Phage Technology
>> Rm 312A, Biochemistry & Biophysics
>> Texas A University
>> College Station, TX 77843
>> e...@tamu.edu
>>
>
>
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Re: [galaxy-dev] tool runner

[Katherine Beaulieu]

On Wed, Aug 3, 2016 at 11:35 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Generally what I've found is that you have to go to another html page and
> in that page's html code you have to specify to go back to galaxy and your
> tool wrapper should take care of submitting to the history. Do you have
> code on github to look at for this?
>
> On Wed, Aug 3, 2016 at 11:07 AM, Mohamed Kassam <k.mam...@gmail.com>
> wrote:
>
>> Dear all,
>>
>> I created a tool in html +pytho, like for the UCSC. My tool is doing a
>> process then return a confirmation of the success of the job.
>>
>> I 'm blocked at the point that I saw that I have to put  method="get" but
>> how to tell to Galaxy to run the job and submit on my history the process.
>>
>> Is there any documentation for the html UCSC part.
>>
>> Best regards,
>>
>> Mohamed
>>
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>
>
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[galaxy-dev] Password Parameter Opinions

[Katherine Beaulieu]

Hi Everyone,
I know this is sort of a controversial topic so I will try to tread
lightly. It seems that for a couple of years the idea of a password
parameter for Galaxy tools has come up a lot but has also been rejected a
lot although I believe there is a lot of merit to it. I have found at least
two other times where people have tried to implement this and it was
rejected, but there must have been a reason why they needed that parameter.
My situation currently is that I have created two tools in Galaxy which
communicate with another software called iRODS which needs authentication
from the user. In my own department, there is another tool that was created
which needed authentication from the user but the developer had to create
some other workaround for this problem.

In terms of the work I have done for this so far, I have been working off
the latest release version of Galaxy. I have implemented the field so that
it is obfuscated in the tool form view as well as on the tool info page. I
will next be looking into storing the parameter in an environment variable
so it doesn't get passed through the command line and encrypting the
password before it enters the database. Speaking with a co-worker of mine,
we discussed the possibility of implementing two option, irreversible
encryption of the password as it gets entered into the database but then
making the tool not workflow compatible, or using regular encryption and
making the tool workflow compatible. I look forward to hearing your
opinions and ideas.

Katherine
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Re: [galaxy-dev] Info Page after tool execution

[Katherine Beaulieu]

Wow thanks for such a quick response!

On Wed, Jul 27, 2016 at 1:22 PM, Dannon Baker <dannon.ba...@gmail.com>
wrote:

> Hi Katherine,
>
> That'd be this method:
> https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/controllers/dataset.py#L978
> Which fills this template:
> https://github.com/galaxyproject/galaxy/blob/dev/templates/show_params.mako
>
> On Wed, Jul 27, 2016 at 1:20 PM Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
>> Hello Galaxy Community,
>> Does anyone know what file would be responsible for creating the info
>> page after the execution of a tool? This is the page you access after
>> output has been created in the history, by clicking on the little 'i' icon.
>> Thanks!
>>
>> ___
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>
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Re: [galaxy-dev] Loading tool config file

[Katherine Beaulieu]

Yes this does help thanks Dannon!:)

On Fri, Jul 22, 2016 at 8:08 AM, Dannon Baker <dannon.ba...@gmail.com>
wrote:

> Hi Katherine,
>
> This all happens in javascript these days, and it's unfortunately a little
> harder to track down all the moving parts than it used to be when this was
> all rendered serverside.  The client requests tool information (like which
> parameters are necessary, etc) from the API, which it then renders using
> the primary tool form found here:
>
> https://github.com/galaxyproject/galaxy/blob/dev/client/galaxy/scripts/mvc/tool
>
> This extends the form code found here:
>
> https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/mvc/form
>
> And individual element types (a select box, for example) can be found here:
>
> https://github.com/galaxyproject/galaxy/tree/dev/client/galaxy/scripts/mvc/ui
>
> Does this help?
>
>
> On Fri, Jul 22, 2016 at 7:40 AM Peter Cock <p.j.a.c...@googlemail.com>
> wrote:
>
>> Sorry, I know relatively little about how Galaxy loads the tool XML
>> files and turns this into the HTML pages. I've mostly searched
>> the codebase with grep at the command line (also searching
>> directly on GitHub works pretty well) trying to trace functionality
>> when I was debugging something.
>>
>> Hopefully one of the Galaxy developers will be able to answer.
>>
>> Peter
>>
>>
>> On Fri, Jul 22, 2016 at 7:29 AM, Katherine Beaulieu wrote:
>> >
>> > No I'm really asking about which files in Galaxy, will load those
>> > parameters on the screen. I believe you were the one to give me a link
>> to
>> > adding a new parameter type in Galaxy via the password parameter, but I
>> > haven't quite been able to implement that. The two files I have changed
>> so
>> > far are basic.py and form_builder.py but using these two files it still
>> only
>> > loads a text parameter.
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[galaxy-dev] Loading tool config file

[Katherine Beaulieu]

Dear all,
I am looking for the files/functions that get called from the point where
you click on the tool name to the point where you get an html version of
your tool on the screen. Could someone indicate what this path looks like?
I would be really appreciative!
Thanks,
Katherine
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Re: [galaxy-dev] Implementing iRODS with Galaxy

[Katherine Beaulieu]

Well I guess this didn't reply to the post I wanted, sorry everyone!

On Mon, Jul 18, 2016 at 6:50 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hi there,
> I have developed a tool that does the importing and exporting to Galaxy.
> Please see the attached link to the github repos for the two tools.
> Please keep in mind that this tool is still in development. As well, it
> has only been tested on a local instance of Galaxy and the authentication
> with iRODS has not quite been worked on. If you have any suggestions please
> let me know.
>
>
> https://github.com/AAFC-MBB/Galaxy/tree/dev/wrappers/irods_pull
> https://github.com/AAFC-MBB/Galaxy/tree/dev/wrappers/irods_push
>
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[galaxy-dev] Implementing iRODS with Galaxy

[Katherine Beaulieu]

Hi there,
I have developed a tool that does the importing and exporting to Galaxy.
Please see the attached link to the github repos for the two tools.
Please keep in mind that this tool is still in development. As well, it has
only been tested on a local instance of Galaxy and the authentication with
iRODS has not quite been worked on. If you have any suggestions please let
me know.


https://github.com/AAFC-MBB/Galaxy/tree/dev/wrappers/irods_pull
https://github.com/AAFC-MBB/Galaxy/tree/dev/wrappers/irods_push
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[galaxy-dev] New galaxy parameter type

[Katherine Beaulieu]

Hi everyone,
I am looking to implement a new parameter type for galaxy tool development.
Does anyone know what would be involved in doing something like this or
perhaps what files would need to be edited?
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Re: [galaxy-dev] Metadata access using tool config

[Katherine Beaulieu]

Actually just figured out the history content api id, just needing the
extra stuff about the job like runtime and start and end times.

On Fri, Jul 8, 2016 at 8:55 AM, Katherine Beaulieu <
katherine.beaulieu...@gmail.com> wrote:

> Hi Greg,
> Thanks for the link to your github repo, some of the information there was
> very useful. Do you have any idea on how to access some of the stuff you
> don't yourself pass to your python script such as the history content api
> id, or the job runtime? For example for the job runtime I feel like it
> should be:
>
> #set job = $input.creating_job
> #set tool_id = $job.runtime
>
> But that just gives an error.
>
> On Thu, Jul 7, 2016 at 12:56 PM, Von Kuster, Greg <g...@psu.edu> wrote:
>
>> Hi Katherine,
>>
>> For the job related stuff, I’m doing this in my tools that provide
>> statistics for the Galaxy ChIP-exo instance I’m setting up for a lab here
>> at Penn State.  You can see variations of tool examples here:
>> https://github.com/gregvonkuster/cegr-galaxy/tree/master/tools/cegr_statistics.
>>  These tools are all included in workflows where the tool is generating
>> metadata about the tool that executed immediatly prior to one of these
>> metadata-generating tools.  I use the while loop in the command to keep the
>> this tool from executing in the workflow before its immediate predecessor
>> is completed.  I assume you are doing something similar, where your tool
>> will generate metadata for some different tool that has already been
>> executed.
>>
>> Here is an example of a basic command line in one of these tool configs
>> that will provide the job stuff to the underlying script.
>>
>> 
>> 
>> 
>>
>> Cheers!
>>
>> Greg Von Kuster
>>
>> On Jul 7, 2016, at 11:40 AM, Katherine Beaulieu <
>> katherine.beaulieu...@gmail.com> wrote:
>>
>> Hi everyone,
>> I am working on a tool which attempts to create a file which stores all
>> the metadata associated with a job execution. The things I know how to
>> access right now are the file extension, name history id, dataset id. I'd
>> like to know how to access other things like the job id, uuid, file size,
>> job command-line, job end time, job start time, core allocated, job runtime
>> and any other important information associated with tool execution. I would
>> prefer to get this information from the tool config file or my tool script
>> and not have the user create an api key which they have to submit as a
>> parameter to my tool. Let me know if you guys have any ideas!
>> Katherine
>> ___
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>> and other Galaxy lists, please use the interface at:
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>>
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>>  http://galaxyproject.org/search/mailinglists/
>>
>>
>>
>
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Re: [galaxy-dev] Metadata access using tool config

[Katherine Beaulieu]

Hi Greg,
Thanks for the link to your github repo, some of the information there was
very useful. Do you have any idea on how to access some of the stuff you
don't yourself pass to your python script such as the history content api
id, or the job runtime? For example for the job runtime I feel like it
should be:

#set job = $input.creating_job
#set tool_id = $job.runtime

But that just gives an error.

On Thu, Jul 7, 2016 at 12:56 PM, Von Kuster, Greg <g...@psu.edu> wrote:

> Hi Katherine,
>
> For the job related stuff, I’m doing this in my tools that provide
> statistics for the Galaxy ChIP-exo instance I’m setting up for a lab here
> at Penn State.  You can see variations of tool examples here:
> https://github.com/gregvonkuster/cegr-galaxy/tree/master/tools/cegr_statistics.
>  These tools are all included in workflows where the tool is generating
> metadata about the tool that executed immediatly prior to one of these
> metadata-generating tools.  I use the while loop in the command to keep the
> this tool from executing in the workflow before its immediate predecessor
> is completed.  I assume you are doing something similar, where your tool
> will generate metadata for some different tool that has already been
> executed.
>
> Here is an example of a basic command line in one of these tool configs
> that will provide the job stuff to the underlying script.
>
> 
> 
> 
>
> Cheers!
>
> Greg Von Kuster
>
> On Jul 7, 2016, at 11:40 AM, Katherine Beaulieu <
> katherine.beaulieu...@gmail.com> wrote:
>
> Hi everyone,
> I am working on a tool which attempts to create a file which stores all
> the metadata associated with a job execution. The things I know how to
> access right now are the file extension, name history id, dataset id. I'd
> like to know how to access other things like the job id, uuid, file size,
> job command-line, job end time, job start time, core allocated, job runtime
> and any other important information associated with tool execution. I would
> prefer to get this information from the tool config file or my tool script
> and not have the user create an api key which they have to submit as a
> parameter to my tool. Let me know if you guys have any ideas!
> Katherine
> ___
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> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
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>
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>
>
>
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[galaxy-dev] Metadata access using tool config

[Katherine Beaulieu]

Hi everyone,
I am working on a tool which attempts to create a file which stores all the
metadata associated with a job execution. The things I know how to access
right now are the file extension, name history id, dataset id. I'd like to
know how to access other things like the job id, uuid, file size, job
command-line, job end time, job start time, core allocated, job runtime and
any other important information associated with tool execution. I would
prefer to get this information from the tool config file or my tool script
and not have the user create an api key which they have to submit as a
parameter to my tool. Let me know if you guys have any ideas!
Katherine
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Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

[Katherine Beaulieu]

Hi Peter, I ending up finding a solution to my problem using this forum
post:
https://lists.galaxyproject.org/pipermail/galaxy-dev/2014-August/020361.html.
I just ended up using the really specific file output path and it started
auto-detecting the file format. Thanks for your help it was much
appreciated.

On Thu, Jun 30, 2016 at 1:01 PM, Peter Cock <p.j.a.c...@googlemail.com>
wrote:

> Maybe sharing your tool XML file would be best - is it on GitHub?
>
> Peter
>
> On Wed, Jun 29, 2016 at 7:43 PM, Katherine Beaulieu
> <katherine.beaulieu...@gmail.com> wrote:
> > Ok, so I don't give the user the option to select the correct data type
> to
> > reduce the amount of stuff the user has to know when using the tool.
> >
> > I do leave the format as auto and Galaxy just leaves it as the generic
> data
> > type 'data'.
> >
> > As for how the format is defined in Galaxy, I'm not quite sure what the
> > answer to this question is because I am just testing the tool with really
> > simple text files, with extension .txt. and it can't seem to pick it up,
> it
> > just leaves it as 'data'. Also not quite sure how to test the Python
> code in
> > the sniff function outside of Galaxy... (only starting working with
> Galaxy 3
> > weeks ago).
> >
> > Let me know if I should provide you with the tool config file if that
> would
> > be a little more useful. It's quite straightforward
> > Thanks for helping with this.
> >
>
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Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

[Katherine Beaulieu]

Ok, so I don't give the user the option to select the correct data type to
reduce the amount of stuff the user has to know when using the tool.

I do leave the format as auto and Galaxy just leaves it as the generic data
type 'data'.

As for how the format is defined in Galaxy, I'm not quite sure what the
answer to this question is because I am just testing the tool with really
simple text files, with extension .txt. and it can't seem to pick it up, it
just leaves it as 'data'. Also not quite sure how to test the Python code
in the sniff function outside of Galaxy... (only starting working with
Galaxy 3 weeks ago).

Let me know if I should provide you with the tool config file if that would
be a little more useful. It's quite straightforward
Thanks for helping with this.

On Wed, Jun 29, 2016 at 11:16 AM, Peter Cock <p.j.a.c...@googlemail.com>
wrote:

> OK. What happens?
>
> Can you select the correct datatype in the upload tool?
> If not, check the file format definition as some file formats
> are configured not to appear here.
>
> Are you leaving the datatype as "auto"? If so, does
> Galaxy fail to identify the file, and leave it as the
> default generic "data" type, or does Galaxy mis-identify
> it as another type?
>
> Have you looked at the Galaxy logs while doing the
> upload?
>
> How is this file format defined in Galaxy? Did you add it?
> Can you test the Python code in the sniff function outside
> of Galaxy to confirm that works?
>
> If Galaxy wrongly picks another fileformat, check where
> in the datatypes_conf.xml is your file format listed? The
> order the sniffing functions are run is important.
>
> Peter
>
> On Wed, Jun 29, 2016 at 3:56 PM, Katherine Beaulieu
> <katherine.beaulieu...@gmail.com> wrote:
> > I am trying to import a file into galaxy.
> >
> > On Wed, Jun 29, 2016 at 10:45 AM, Peter Cock <p.j.a.c...@googlemail.com>
> > wrote:
> >>
> >> The auto-detection is only used when importing a
> >> file into Galaxy (e.g. by uploading it).
> >>
> >> If you are writing a tool which produces output in your
> >> format, then the tool's XML should specify that output
> >> format.
> >>
> >> Which of these are you trying to do? Or both?
> >>
> >> Peter
> >>
> >> On Wed, Jun 29, 2016 at 3:36 PM, Katherine Beaulieu
> >> <katherine.beaulieu...@gmail.com> wrote:
> >> > Hmm, I must have some sort of other logic error which is preventing
> the
> >> > detection of the format. Thanks for the information!
> >> >
> >> > On Wed, Jun 29, 2016 at 10:24 AM, Peter Cock <
> p.j.a.c...@googlemail.com>
> >> > wrote:
> >> >>
> >> >> Have you invented your own file format, or are you using
> >> >> an existing file format defined within Galaxy?
> >> >>
> >> >> The Galaxy file formats with automatic detection are all
> >> >> defined via Python classes which define a sniff method.
> >> >>
> >> >> Peter
> >> >>
> >> >> On Wed, Jun 29, 2016 at 3:15 PM, Katherine Beaulieu
> >> >> <katherine.beaulieu...@gmail.com> wrote:
> >> >> > Hi everyone,
> >> >> > I am looking to auto-detect the file format of a file outputted by
> a
> >> >> > python
> >> >> > tool I have written. Does anyone have any idea how to do this? I
> have
> >> >> > tried
> >> >> > setting the format attribute to "auto" with no luck. Let me know if
> >> >> > you
> >> >> > would like to see my tool config file.
> >> >> > Cheers,
> >> >> > Katherine
> >> >> >
> >> >> > ___
> >> >> > 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:
> >> >> >   https://lists.galaxyproject.org/
> >> >> >
> >> >> > To search Galaxy mailing lists use the unified search at:
> >> >> >   http://galaxyproject.org/search/mailinglists/
> >> >
> >> >
> >
> >
>
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[galaxy-dev] Auto detection of output format Galaxy custom tool

[Katherine Beaulieu]

Hi everyone,
I am looking to auto-detect the file format of a file outputted by a python
tool I have written. Does anyone have any idea how to do this? I have tried
setting the format attribute to "auto" with no luck. Let me know if you
would like to see my tool config file.
Cheers,
Katherine
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