[galaxy-dev] Adding a new web-service or perhaps a "webapp" to Galaxy

[Lukasse, Pieter]

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

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Re: [galaxy-dev] Adding a new web-service or perhaps a "webapp" to Galaxy

[Lukasse, Pieter]

I could add a new file to

/lib/galaxy/webapps/galaxy/controllers/

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


From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf 
Of Lukasse, Pieter
Sent: vrijdag 9 januari 2015 13:28
To: galaxy-...@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

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[galaxy-dev] FW: Adding a new web-service or perhaps a "webapp" to Galaxy

[Lukasse, Pieter]

Meanwhile I added a new file indeed to 
/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-boun...@lists.galaxyproject.org] On Behalf 
Of Lukasse, Pieter
Sent: vrijdag 9 januari 2015 13:55
To: galaxy-...@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

/lib/galaxy/webapps/galaxy/controllers/

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


From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf 
Of Lukasse, Pieter
Sent: vrijdag 9 januari 2015 13:28
To: galaxy-...@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

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nist_controller.py
Description: nist_controller.py
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[galaxy-dev] galaxy-central and nginx

[Jorrit Boekel]

Hi all,

I’m testing the latest galaxy-central (rev 15961:63d901ca0e6e) to try out 
dataset collections. First thing I run into is that things don’t seem to run 
well when running it on a VM (port forwarded) with nginx. If I click on tools I 
get a white screen instead of tool options, and the log show an error from 
lib/galaxy/webapps/galaxy/api/tools.py : Checking parameter file failed.

The setup: URL would be galaxydomain.com:3030, which the VM manager forwards to 
port 80 on the galaxy VM, which there nginx would forward to port 8080. Now, my 
nginx is set up to work with older galaxy versions, I don’t know if that 
matters. I haven’t changed any config files at all yet.

When I turn off nginx and serve directly on port 80 (using sudo), things look 
like they work. At least the tools look like they should. Has the nginx config 
to use changed recently or is this some weird artefact? Anyone else seen it? 
Since I’m just goofing around to see how collections work, it is not the end of 
the world for me, and I know galaxy-dist is the stable one, but still.

cheers,
— 
Jorrit Boekel
Proteomics systems developer
BILS / Lehtiö lab
Scilifelab Stockholm, Sweden



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Re: [galaxy-dev] Galaxy Bioblend option for importing dataset into a library?

[Nicola Soranzo]

Hi Damion,
I finally got to implement this, see method copy_from_dataset() in this
commit:

https://github.com/afgane/bioblend/commit/bc6b7cb71abb25aa109b85b1ff24e73aadac5ce4

Best,
Nicola

Il 06.10.2014 17:59 Nicola Soranzo ha scritto:
Il giorno gio, 02/10/2014 alle 16.50 -0700, Dooley, Damion ha 
scritto:



I see Galaxy API has a feature to import a history dataset into the
library (in copy_hda_to_ldda() fn from GCC2013 training day course). 
Is
this available as well via Bioblend? Latest docs don't seem to 
include

this feature. It would be the opposite of Bioblend's
upload_dataset_from_library(history_id, lib_dataset_id) )


Hi Damion,
indeed this feature is not in BioBlend yet, but I have it in my TODO
list because we also need it. Hopefully I'll soon have some time to
implement the method, test it and open a PR.

Best,
Nicola

Objective is to get customized blast indexes into library that way 
for
shared use. Or have them actually exist outside galaxy, and linked 
in.


Regards,

Damion

Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC 
Centre for Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 
Canada



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[galaxy-dev] Tool Development DELLY

[Marco Albuquerque]

Hello Galaxy,

I'm currently working on adding some tools and am having an issue with
DELLY.

So, I am under the impression that BAM indexing happens automatically when a
BAM is uploaded. However there is no associated dataset_i.dat.bai file in
the file location in my local instance of galaxy.

There is however metadata which seems to be created but they are not being
linked together. What I mean to say is DELLY errors with cannot find Bam
Index.

I was curious if there is a specific way developers are suppose to work
around this? Basically we want to avoid having to provide both the BAM and
BAM index and symbolically linking a new dataset because we know you have
already created a better implementation, we just want to use it and don't
know how.

Any help is greatly appreciated,

Marco


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Re: [galaxy-dev] Tool Development DELLY

[Peter Cock]

On Thu, Jan 8, 2015 at 6:11 PM, Marco Albuquerque
 wrote:
> Hello Galaxy,
>
> I'm currently working on adding some tools and am having an issue with
> DELLY.
>
> So, I am under the impression that BAM indexing happens automatically when a
> BAM is uploaded. However there is no associated dataset_i.dat.bai file in
> the file location in my local instance of galaxy.
>
> There is however metadata which seems to be created but they are not being
> linked together. What I mean to say is DELLY errors with cannot find Bam
> Index.
>
> I was curious if there is a specific way developers are suppose to work
> around this? Basically we want to avoid having to provide both the BAM and
> BAM index and symbolically linking a new dataset because we know you have
> already created a better implementation, we just want to use it and don't
> know how.
>
> Any help is greatly appreciated,
>
> Marco

I think the symlink approach is best, see for example the Python
wrapper script I used here for "samtools idxstats",
https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats

However, you can make the link in the XML directly, see Dave's
reworking of this wrapper:
https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/samtools/samtools_idxstats

Regards,

Peter
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