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

h 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 wo

[galaxy-dev] Password Parameter Opinions

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

Re: [galaxy-dev] Deprecated code file tag

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 di

Re: [galaxy-dev] tool runner

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 car

[galaxy-dev] Galaxy URL and api key tool config

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 ___ Please keep all replies on the list by

[galaxy-dev] New galaxy parameter type

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? ___ Please keep all replies on the

Re: [galaxy-dev] Implementing iRODS with Galaxy

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 lin

[galaxy-dev] Implementing iRODS with Galaxy

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

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

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: &g

[galaxy-dev] Metadata access using tool config

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

Re: [galaxy-dev] Metadata access using tool config

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!

Re: [galaxy-dev] Metadata access using tool config

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 githu

[galaxy-dev] Parameter Storing in Database

Would anyone be able to tell me in what file the storing of tool parameters into the database occurs? Thanks! Katherine ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this

Re: [galaxy-dev] Loading tool config file

gt; 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 >&

[galaxy-dev] Loading tool config file

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

[galaxy-dev] Auto detection of output format Galaxy custom tool

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

Re: [galaxy-dev] Auto detection of output format Galaxy custom tool

ide > 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, Kathe

[galaxy-dev] Check running jobs

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

Re: [galaxy-dev] Check running jobs

b/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>

Re: [galaxy-dev] Check running jobs

mail). > > 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 run

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

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

[galaxy-dev] Workflow ID, Galaxy Instance URL, API Key in Galaxy Tool Config

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

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

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 pai

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

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 ca

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

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

[galaxy-dev] How to set up handler and web server process within a virtual machine

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

[galaxy-dev] Parameters out

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 ___ Please

Re: [galaxy-dev] Parameters out

ugh 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 > >

[galaxy-dev] Batch Mode Tool Execution

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 ___ Please

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

, 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 th

Re: [galaxy-dev] Modifying Values in the Database

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 > &

Re: [galaxy-dev] Parameter Storing in Database

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

[galaxy-dev] Workflow Compatibility

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

Re: [galaxy-dev] Workflow Compatibility

erent 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 Beaulie

Re: [galaxy-dev] Workflow Compatibility

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 thi

Re: [galaxy-dev] Workflow Compatibility

ed, 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, Kat

[galaxy-dev] Workflow Execution Files

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

[galaxy-dev] Fwd: Workflow Execution Files

-- 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

Re: [galaxy-dev] Storing data in the user session

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.

Re: [galaxy-dev] Galaxy on the Cloud with Openstack

ernals 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, >> Do

[galaxy-dev] Code File Execution

Hi Everyone, Does anyone know how execution of code files happens? Is there a function somewhere that fills the parameters in? Cheers, Katherine ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your

[galaxy-dev] Job_id in a galaxy tool

Hello Galaxy Community, Is it possible to get the job_id listed on the info 'eye' page within a tool wrapper? Katherine ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this