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.gruening@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:greg@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-dev@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.lukasse@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-par ty_tool_dependency_installation_and_compilation_with_installed_reposit 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
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