Re: [galaxy-dev] Changing tool panel ordering [was:] HOWTO for making new toolshed package

12 Sep 2013

      Hi Bjoern,

Thanks, that is helpful information. Updates to new revisions seem to work fine, i.e. the order as configured in shed_tool_conf.xml seems to be preserved. 

We are now facing what I think could be a small bug in the $PATH_TO_IMAGES part as documented in http://wiki.galaxyproject.org/ToolShedToolFeatures#Properly_defining_the_loc...

We get the tool UI rendered but without the images in the documentation section. When looking at the URL in this section we find the following: 

http://10.73.10.111/galaxy_testing/$PATH_TO_IMAGES/napq_overview.png 

so the variable is not being replaced by the value of the path...is this a known issue?

Regards,

Pieter.

-----Original Message-----
From: Bjoern Gruening [mailto:bjoern.gruening@gmail.com] 
Sent: donderdag 12 september 2013 14:31
To: Lukasse, Pieter
Cc: 'Greg Von Kuster'; Galaxy Dev
Subject: Changing tool panel ordering [was:] HOWTO for making new toolshed package

Hi Pieter,

to manipulate the ordering of tools is currently not trivial, as far as I know. You can add label into your shed_tool_conf.xml and tool_conf.xml file and they should appear and stay. The final ordering will be a merge of all your *_tool_conf.xml files into the integrated_tool_panel.xml. If you change that file you will see that the ordering will change, but that file can be overwritten. 

I would play with the shed_tool_conf.xml and tool_conf.xml, try to reorder your tools and delete the integrated_tool_panel.xml file. After restarting you will see the effects.

In each case, the admin needs to do that.

I have a pull request that enables dynamic filtering of tools by the user, maybe you are interested in testing:

https://bitbucket.org/galaxy/galaxy-central/pull-request/179/implement-the-a...

Cheers,
Bjoern
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One extra detail I'm trying to find in the docs but haven't found yet:
How can I ensure that the tools of my package are presented in a 
specific order in the menu panel item I selected during install? And 
is it possible to define some labels to appear between the tools 
(Something like the screenshot below)? Or is this something the admin 
should configure in shed_tool_conf.xml? And will this order 
configuration be kept also when new versions of the tools are 
installed?
Example:
-----Original Message-----
From: Greg Von Kuster [mailto:greg@bx.psu.edu]
Sent: donderdag 12 september 2013 13:27
To: Lukasse, Pieter
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] HOWTO for making new toolshed package
This scenario should be hopefully handled by the automated nightly 
tests that run on repositories in the test and main Galaxy tool sheds.
This test framework does not yet provide full coverage, but it 
eventually will.  Each repository that has been tested includes a 
"Tool test results" container when viewing or managing the repository.
Greg Von Kuster
On Sep 12, 2013, at 7:23 AM, "Lukasse, Pieter" <pieter.lukasse@wur.nl>
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Ok, cool...I get the picture.
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One small downside is that then admin has to trust the developer has
the discipline and sound judgment to correctly increase version 
numbers when applicable....I'm just thinking of scenarios where there 
is a "bad update" released and the admin would like to quickly revert 
back to the previous revision after noticing that this update has an 
unexpected bug....
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Regards,
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Pieter.
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-----Original Message-----
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From: Bjoern Gruening [mailto:bjoern.gruening@gmail.com]
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Sent: donderdag 12 september 2013 13:15
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To: Lukasse, Pieter
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Cc: 'Greg Von Kuster'; Galaxy Dev
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Subject: Re: [galaxy-dev] HOWTO for making new toolshed package
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Hi Pieter,
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yes that is possible. Have a look at other repositories. You can
only choose between different tool versions, it there are more than 
one 'installable version' of a tool. It is not the case in your 
example.
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Lets imagine I only fix some help text in the tool. I do not want to
have separated version, I would prefer to just update the tool in 
place.
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But if I change a version number or increase the dependency version
I would like a new 'installable version' of my tool. The toolshed can 
distinguish between such cases.
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Cheers,
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Bjoern
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Hi Greg,
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Fantastic, thanks for your detailed answer!
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I am trying out some things and I noticed that it is not possible
to
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select a specific revision of a repository for installation (see
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screenshot). I thought I saw you present something like this at
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Oslo...is that possible ?
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Regards,
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Pieter.
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From: Greg Von Kuster [mailto:greg@bx.psu.edu]
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Sent: woensdag 11 september 2013 19:25
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To: Lukasse, Pieter
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Cc: Galaxy Dev
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Subject: Re: HOWTO for making new toolshed package
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Hello Pieter,
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Please send questions like this to the galaxy-dev@bx.psu.edu or
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galaxy-dev@lists.bx.psu.edu mailing list rather than individual
email
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addresses to ensure optimal, timely responses.
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The Tool Shed wiki contains all of the information you need:
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http://wiki.galaxyproject.org/Tool%20Shed
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This page provides a nice overview of repository features:
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http://wiki.galaxyproject.org/ToolShedRepositoryFeatures
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See additional specific pages below for each item you've listed:
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On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter"
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<pieter.lukasse@wur.nl> wrote:
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Hi Greg,
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I want to make a toolshed package with the following contents:
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The above "package" is actually a mercurial repository in the tool
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·         A number of tools
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The following pages will provide all of the information you'll
need
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for building Galaxy tools for the Tool Shed.
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http://wiki.galaxyproject.org/ToolShedToolFeatures
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·         Some workflows
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The following pages provide information for enabling workflow
sharing
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via the Tool Shed.
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http://wiki.galaxyproject.org/ToolShedWorkflowSharing
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·         Datatypes
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Datatype features in the Tool Shed are described in the following
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pages:
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http://wiki.galaxyproject.org/ToolShedDatatypesFeatures
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·         Installation configurations for installing external tools
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like R, Gnuplot and X!Tandem
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The above information is document in the "ToolShedToolFeatures"
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section of the wiki, specifically in the following pages:
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http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-pa
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ty_tool_dependency_installation_and_compilation_with_installed_reposi
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ories
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·         Dependencies configurations to other packages
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If by "packages", you are referring to other tool shed
repositories,
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then the documentation describing defining these relationships is
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located in the following pages:
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http://wiki.galaxyproject.org/DefiningRepositoryDependencies
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Is there a HOWTO wiki page where I can find exactly which files I
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should add to the .zip file and how they should be named? Or maybe
an
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example package which I could use?
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Regards,
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Pieter Lukasse
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Wageningen UR, Plant Research International
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Departments of Bioscience and Bioinformatics
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Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
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Wageningen, the Netherlands
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+31-317480891; skype: pieter.lukasse.wur
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http://www.pri.wur.nl
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___________________________________________________________
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:
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