Hello Pieter, Bjoern is correct here for tools, and the same behavior occurs for other Galaxy utilities that may be contained in tool shed repositories ( e.g., tool dependency definitions, repository dependency definitions, custom datatypes, etc ). Each type of Galaxy utility is associated with a set of rules that define whether changes to the utility result in a new installable changeset revision or not. Greg Von Kuster On Sep 12, 2013, at 7:14 AM, Bjoern Gruening <bjoern.gruening@gmail.com> wrote:
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-party_too...
· 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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