Re: [galaxy-dev] HOWTO for making new toolshed package

12 Sep 2013

      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:

[cid:image001.png@01CEAFC3.5DFF77B0]

-----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<mailto:pieter.lukasse@wur.nl>> wrote:
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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<mailto:galaxy-dev@bx.psu.edu> or
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galaxy-dev@lists.bx.psu.edu<mailto: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<mailto: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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*         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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___________________________________________________________
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Please keep all replies on the list by using "reply all"
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in your mail client.  To manage your subscriptions to this and other
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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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