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_location_of_images_in_tool_configuration_files

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.gruen...@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-ability-to-change-the-tool/diff

Cheers,
Bjoern



> 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:g...@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.luka...@wur.nl>
> wrote:
> 
>  
> 
> > Ok, cool...I get the picture. 
> 
> > 
> 
> > 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....
> 
> > 
> 
> > Regards,
> 
> > 
> 
> > Pieter.
> 
> > 
> 
> > -----Original Message-----
> 
> > From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]
> 
> > Sent: donderdag 12 september 2013 13:15
> 
> > To: Lukasse, Pieter
> 
> > Cc: 'Greg Von Kuster'; Galaxy Dev
> 
> > Subject: Re: [galaxy-dev] HOWTO for making new toolshed package
> 
> > 
> 
> > Hi Pieter,
> 
> > 
> 
> > 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.
> 
> > 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.
> 
> > 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.
> 
> > 
> 
> > Cheers,
> 
> > Bjoern
> 
> > 
> 
> >> Hi Greg,
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> Fantastic, thanks for your detailed answer! 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> I am trying out some things and I noticed that it is not possible
> to
> 
> >> select a specific revision of a repository for installation (see
> 
> >> screenshot). I thought I saw you present something like this at
> 
> >> Oslo...is that possible ?
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> Regards,
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> Pieter.
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> From: Greg Von Kuster [mailto:g...@bx.psu.edu]
> 
> >> Sent: woensdag 11 september 2013 19:25
> 
> >> To: Lukasse, Pieter
> 
> >> Cc: Galaxy Dev
> 
> >> Subject: Re: HOWTO for making new toolshed package
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> Hello Pieter,
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> Please send questions like this to the galaxy-...@bx.psu.edu or
> 
> >> galaxy-dev@lists.bx.psu.edu mailing list rather than individual
> email
> 
> >> addresses to ensure optimal, timely responses.
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> The Tool Shed wiki contains all of the information you need:
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> http://wiki.galaxyproject.org/Tool%20Shed
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> This page provides a nice overview of repository features:
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> http://wiki.galaxyproject.org/ToolShedRepositoryFeatures
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> See additional specific pages below for each item you've listed:
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> On Sep 11, 2013, at 11:52 AM, "Lukasse, Pieter"
> 
> >> <pieter.luka...@wur.nl> wrote:
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> Hi Greg,
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> I want to make a toolshed package with the following contents:
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> The above "package" is actually a mercurial repository in the tool
> 
> >> shed.
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >>        ·         A number of tools
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> The following pages will provide all of the information you'll
> need
> 
> >> for building Galaxy tools for the Tool Shed.
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> http://wiki.galaxyproject.org/ToolShedToolFeatures
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >>        ·         Some workflows
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> The following pages provide information for enabling workflow
> sharing
> 
> >> via the Tool Shed.
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> http://wiki.galaxyproject.org/ToolShedWorkflowSharing
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> ·         Datatypes
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> Datatype features in the Tool Shed are described in the following
> 
> >> pages:
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> http://wiki.galaxyproject.org/ToolShedDatatypesFeatures
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> ·         Installation configurations for installing external tools
> 
> >> like R, Gnuplot and X!Tandem
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> The above information is document in the "ToolShedToolFeatures" 
> 
> >> section of the wiki, specifically in the following pages:
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >>
> http://wiki.galaxyproject.org/ToolShedToolFeatures#Automatic_third-pa
> 
> >> r
> 
> >>
> ty_tool_dependency_installation_and_compilation_with_installed_reposi
> 
> >> t
> 
> >> ories
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> ·         Dependencies configurations to other packages
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> If by "packages", you are referring to other tool shed
> repositories,
> 
> >> then the documentation describing defining these relationships is
> 
> >> located in the following pages:
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> http://wiki.galaxyproject.org/DefiningRepositoryDependencies
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> Is there a HOWTO wiki page where I can find exactly which files I
> 
> >> should add to the .zip file and how they should be named? Or maybe
> an
> 
> >> example package which I could use?
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> Regards,
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> Pieter Lukasse
> 
> >> 
> 
> >> Wageningen UR, Plant Research International
> 
> >> 
> 
> >> Departments of Bioscience and Bioinformatics
> 
> >> 
> 
> >> Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB,
> 
> >> Wageningen, the Netherlands
> 
> >> 
> 
> >> +31-317480891; skype: pieter.lukasse.wur
> 
> >> 
> 
> >> http://www.pri.wur.nl
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> 
> 
> >> ___________________________________________________________
> 
> >> 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:
> 
> >>  http://lists.bx.psu.edu/
> 
> >> 
> 
> >> To search Galaxy mailing lists use the unified search at:
> 
> >>  http://galaxyproject.org/search/mailinglists/
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > 
> 
> > ___________________________________________________________
> 
> > 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:
> 
> >  http://lists.bx.psu.edu/
> 
> > 
> 
> > To search Galaxy mailing lists use the unified search at:
> 
> >  http://galaxyproject.org/search/mailinglists/
> 
> > 
> 
>  
> 
>  
> 
> 
> ___________________________________________________________
> 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:
>   http://lists.bx.psu.edu/
> 
> To search Galaxy mailing lists use the unified search at:
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