Re: [galaxy-dev] Suggestion for Structural Variant Analysis onto Galaxy Main

Hi Orlando, please fill your requests here: https://github.com/galaxyproject/tools-iuc/issues/ A list of tools and if you have the Test Tool Shed links if there is already preliminary work. We can also kickstart you if you want to integrate your own tools into Galaxy. Thanks! Bjoern Am

Re: [galaxy-dev] planemo shed_create bug? on planemo/server docker image

Am 14.07.2016 um 09:33 schrieb Steve Cassidy: > Hi Bjorn, thanks for the response, very happy to go with the future > way of doing things. I did see the references to conda but couldn’t > quite decipher what was needed. > > Are you saying that I should create a new recipe in bioconda for my >

[galaxy-dev] Fwd: New galaxy parameter type

forwarding to the list -- Forwarded message - From: Katherine Beaulieu Date: Fri, Jul 15, 2016 at 3:45 PM Subject: Re: [galaxy-dev] New galaxy parameter type To: Martin Čech Thanks Peter, I will look into that. The reason I

Re: [galaxy-dev] New galaxy parameter type

Katherine please disregard my answer, I probably misread your question. :) M. On Fri, Jul 15, 2016 at 3:05 PM Peter Cock wrote: > Did you mean parameter as in input field shown > to the user? Like a combobox or text field? > > Since this happened to come up earlier

Re: [galaxy-dev] New galaxy parameter type

Did you mean parameter as in input field shown to the user? Like a combobox or text field? Since this happened to come up earlier today, here's a rejected pull request which added a password parameter - that ought to give you a rough idea: https://github.com/galaxyproject/galaxy/pull/393 Peter

Re: [galaxy-dev] New galaxy parameter type

Hi Katherine, an example of a datatype addition can be seen in this PR: https://github.com/galaxyproject/galaxy/pull/2452 You need to define a class and teach it to sniff files of your defined type (with a doctest) and how to generate peek for the datatype's datasets in history. Let us know if

[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

[galaxy-dev] Suggestion for Structural Variant Analysis onto Galaxy Main

Hello Galaxy dev I would like to suggest the idea of adding structural variant analysis tools for large structural variations for detecting long insertions, inversions or translocations on to the Galaxy Main. Currently, there are tools for detecting small variants, less than 50 bp for small

Re: [galaxy-dev] package_cython_0_20_1

Cool thanks that was quick… From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola Soranzo Sent: Friday, July 15, 2016 3:24 PM To: Rathert, Philipp, Dr. ; galaxy-dev@lists.galaxyproject.org Subject: Re: [galaxy-dev]

Re: [galaxy-dev] default number of concurrent jobs

copy job_conf.xml.sample_basic to job_conf.xml and make the changes (and restart galaxy) Hans-Rudolf On 07/15/2016 10:32 AM, Ulf Schaefer wrote: Hi Hans-Rudolf That was the first thing that came to my mind as well. But by default you don't seem to get a "job_conf.xml". You just get

Re: [galaxy-dev] package_cython_0_20_1

Hi Philipp, I have updated the package on the ToolShed, can you try to update it on your local Galaxy and reinstall the dependency? Cheers, Nicola On 15/07/16 12:24, Rathert, Philipp, Dr. wrote: package_cython_0_20_1 Dear all, I am trying to install package_cython_0_20_1 but I always get

Re: [galaxy-dev] Get the username and password of a user

Hi Mohamed, See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax which explains the $__user_id__ and $__user_email__ tokens which can be used in the definition of a tool wrapper XML file. From a security point of view, I don't think any tool should have access to the user's Galaxy

[galaxy-dev] Get the username and password of a user

Dear all, I would like to know if there is ana api which I can get the password and username of a user directly for my python code. I would like to send these infromation to an another server for connection. Thanks in advance ___ Please keep

Re: [galaxy-dev] hide password xml tag

Hello I am encrypted the password in my python file, because I need to connect to other system. So there is no other way do not show password when I am typing in the html. Thanks 2016-07-15 10:44 GMT+02:00 Peter Cock : > This has been suggested before (with code to

Re: [galaxy-dev] hide password xml tag

This has been suggested before (with code to do it), but rejected on security grounds, see: https://github.com/galaxyproject/galaxy/pull/393 What would you do with the password when calling your tool? If you use it directly in the command line string then it will appear in the Galaxy logs, but

Re: [galaxy-dev] default number of concurrent jobs

Hi Hans-Rudolf That was the first thing that came to my mind as well. But by default you don't seem to get a "job_conf.xml". You just get "job_conf.xml.sample_advanced" and "job_conf.xml.sample_basic", so I assume it is not really using any of those two. However in the

[galaxy-dev] hide password xml tag

Dear all, I would like to hide when typing a password in a tool I develloped. Do you have the tag I have to use, I tried type="password" but it does not work. Thanks in advance, ___ Please keep all replies on the list by using "reply all" in

Re: [galaxy-dev] default number of concurrent jobs

Hi Ulf Have a look at the "job_conf.xml" file, see also: https://wiki.galaxyproject.org/Admin/Config/Jobs Regards, Hans-Rudolf On 07/14/2016 01:35 PM, Ulf Schaefer wrote: Hi all I installed an out-of-the-box Galaxy instance on my local machine as per the instructions