Hi Greg, I would like to deploy my custom controller together with my tool via toolshed. Is there already a way to do this? What should I add to my tool_dependencies.xml? I tried something like : <action type="shell_command"> cd $GALAXY_HOME; wget http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/nist_wrapper/raw-file/tip/...; </action> But I'm glad this apparently didn't work ;) Thanks, Pieter From: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] On Behalf Of Lukasse, Pieter Sent: vrijdag 9 januari 2015 16:10 To: 'galaxy-dev@lists.galaxyproject.org' Subject: [galaxy-dev] FW: Adding a new web-service or perhaps a "webapp" to Galaxy Meanwhile I added a new file indeed to <galaxy-dist>/lib/galaxy/webapps/galaxy/controllers/ and this works for me. If there is a better/easier/standard way of doing this, please let me know! Attached my file as example. Best regards, Pieter From: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] On Behalf Of Lukasse, Pieter Sent: vrijdag 9 januari 2015 13:55 To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] Adding a new web-service or perhaps a "webapp" to Galaxy I could add a new file to <galaxy-dist>/lib/galaxy/webapps/galaxy/controllers/ ...is that a good way to do it? From: galaxy-dev [mailto:galaxy-dev-bounces@lists.galaxyproject.org] On Behalf Of Lukasse, Pieter Sent: vrijdag 9 januari 2015 13:28 To: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: [galaxy-dev] Adding a new web-service or perhaps a "webapp" to Galaxy Hi, In one of my tools I generate a HTML report which I would like to enhance with some ajax functionality. I would like the possibility to do some backend computations based on the ajax requests. My question is: is there an easy way to add a new web-service to my Galaxy server? The web-service implementation would be in python. Ideally I would like to be able to ship this python file together with my tool via tool shed (and when installing from toolshed, the necessary configurations are applied to the server to enable this python code as a local web-service on the respective Galaxy server). Thanks! Pieter Lukasse Wageningen UR, Plant Research International Department of Bioinformatics (Bioscience) Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

Pieter, As Martin said, a data source tool would be your best approach. This is fairly simple to implement, all you need is a standard tool with no input datasets and one parameter for the CAS registry number. That number gets plugged into a script called in the command tag, e.g. <command interpreter="python">get_nist.py --cas_id "$input_id" --output "$output_dataset"</command> Inside get_nist.py, you'll want code that takes the CAS number and builds the URL to get mass spectrometry or other data, then parses the returned information, writing the data to the filename passed in the command line. One thing to consider is that if you have a free-form text entry field for the CAS number, you may want to add a filter to only allow printable characters, or numbers, or whichever bytes are allowed for those identifiers. If you'd like specific advice on any of those items, feel free to contact me. --Dave B. On 01/23/2015 10:56 AM, Martin Čech wrote:

Hello Pieter,

adding a controller to Galaxy's codebase is not possible through the Tool Shed. It would be very unsecure to allow such.

However, reading your code (https://gist.github.com/martenson/7ce1ddb19c199b2df61c) you should be able to convert this controller into an actual tool (data source tool kind) pretty easily and publishing the tool through the Tool Shed should be straight forward afterwards.

Dave Bouvier will get back to you with some tips in the next message.

Thank you for using Galaxy.

Martin

On Fri Jan 23 2015 at 8:36:44 AM Lukasse, Pieter <pieter.lukasse@wur.nl <mailto:pieter.lukasse@wur.nl>> wrote:

Hi Greg,____

__ __

I would like to deploy my custom controller together with my tool via toolshed. Is there already a way to do this? What should I add to my tool_dependencies.xml?____

__ __

I tried something like :____

__ __

<actiontype=/"shell_command"/>____

_cd_ $GALAXY_HOME;____

_wget_ http://toolshed.g2.bx.psu.edu/__repos/pieterlukasse/nist___wrapper/raw-file/... <http://toolshed.g2.bx.psu.edu/repos/pieterlukasse/nist_wrapper/raw-file/tip/nist_controller.py>;____

</action>____

__ __

But I’m glad this apparently didn’t work ;)____

__ __

Thanks,____

__ __

Pieter____

__ __

*From:*galaxy-dev [mailto:galaxy-dev-bounces@__lists.galaxyproject.org <mailto:galaxy-dev-bounces@lists.galaxyproject.org>] *On Behalf Of *Lukasse, Pieter *Sent:* vrijdag 9 januari 2015 16:10 *To:* 'galaxy-dev@lists.__galaxyproject.org <mailto:galaxy-dev@lists.galaxyproject.org>' *Subject:* [galaxy-dev] FW: Adding a new web-service or perhaps a "webapp" to Galaxy____

__ __

Meanwhile I added a new file indeed to <galaxy-dist>/lib/galaxy/__webapps/galaxy/controllers/____

and this works for me. If there is a better/easier/standard way of doing this, please let me know! ____

__ __

Attached my file as example.____

__ __

Best regards,____

__ __

Pieter____

__ __

*From:*galaxy-dev [mailto:galaxy-dev-bounces@__lists.galaxyproject.org <mailto:galaxy-dev-bounces@lists.galaxyproject.org>] *On Behalf Of *Lukasse, Pieter *Sent:* vrijdag 9 januari 2015 13:55 *To:* galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu> *Subject:* Re: [galaxy-dev] Adding a new web-service or perhaps a "webapp" to Galaxy____

__ __

I could add a new file to ____

__ __

<galaxy-dist>/lib/galaxy/__webapps/galaxy/controllers/ ____

__ __

...is that a good way to do it?____

__ __

__ __

*From:*galaxy-dev [mailto:galaxy-dev-bounces@__lists.galaxyproject.org <mailto:galaxy-dev-bounces@lists.galaxyproject.org>] *On Behalf Of *Lukasse, Pieter *Sent:* vrijdag 9 januari 2015 13:28 *To:* galaxy-dev@lists.bx.psu.edu <mailto:galaxy-dev@lists.bx.psu.edu> *Subject:* [galaxy-dev] Adding a new web-service or perhaps a "webapp" to Galaxy____

__ __

Hi,____

__ __

In one of my tools I generate a HTML report which I would like to enhance with some ajax functionality. I would like the possibility to do some backend computations based on the ajax requests. ____

__ __

My question is: is there an easy way to add a new web-service to my Galaxy server? The web-service implementation would be in python. Ideally I would like to be able to ship this python file together with my tool via tool shed (and when installing from toolshed, the necessary configurations are applied to the server to enable this python code as a local web-service on the respective Galaxy server). ____

__ __

Thanks!____

__ __

Pieter Lukasse____

Wageningen UR, Plant Research International____

Department of Bioinformatics (Bioscience)____

Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands____

T: +31-317481122; M: +31-628189540; skype: pieter.lukasse.wur____

http://www.pri.wur.nl <http://www.pri.wur.nl/>____

__ __

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