Hi Peter,

On Mar 4, 2014, at 5:19 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> On Mon, Mar 3, 2014 at 6:33 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> On Mar 3, 2014, at 1:13 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
>> 
>>> Hi Guys,
>>> 
>>> Is this stuff on the wiki?
>> 
>> Not completely yet.
> 
> The only mention I found was something in passing on last
> month's news page:
> https://wiki.galaxyproject.org/DevNewsBriefs/2014_02_10

Unfortunately I was not able to complete my usual level of documentation in the 
Tool Shed wiki for inclusion in the Galaxy News Brief for the last release (my 
plate was too full at the time).

I've introduced the feature in the following article - this is the venue I will 
use going forward for the Tool Shed.

http://gregvonkuster.org/galaxy-tool-shed-primary-repository-features/


> 
>>> Presumably the goal is helping to
>>> move repositories between Tool Shed instances (e.g. from
>>> a development/private Tool Shed to a production/public
>>> Tool Shed)?
>> 
>> Yes.
> 
> How do these "capsules" differ from the standard tar-ball?
> Is it effectively the tar-ball contents plus the repository meta
> data like its description and keywords?

From the above article:

Export this revision

This feature is available to all Tool Shed accounts.  It will inspect the 
selected repository revision and create a compressed archive of files that can 
be imported into another Tool Shed.  I’ve called this archive a repository 
capsule.  This feature streamlines the Galaxy utility development process for 
the Tool Shed in that it allows for an entire repository dependency hierarchy 
to easily be moved from one Tool Shed to another.  For example, a repository 
capsule could be exported from a local development Tool Shed and imported into 
the Test Tool Shed hosted by the Galaxy Development Team.  Similarly, a capsule 
could be exported from the Test Tool Shed and imported into the Main Tool Shed. 
 All of the repository’s defined repository dependencies can optionally be 
included in the same capsule.

An XML file named manifest.xml is automatically created and included in the 
capsule.  This file contains the entire list of repositories contained within 
the capsule and the order in which they must be imported into a Tool Shed.  
This file also includes information about each repository (e.g.,the repository 
owner and revision) as well as the Tool Shed categories associated with each of 
them.  The Tool Shed into which the capsule is imported will be inspected to 
see if any of the contained repositories already exists.  Those that do will 
not be overwritten or altered in any way.  A repository created in a Tool Shed 
from an imported capsule will be defined as installable only if its creation 
resulted in no errors.

Since repositories that were exported into a capsule are associated with a user 
(the owner), the user importing the capsule into a Tool Shed must be authorized 
to create the repository in that Tool Shed with that specific owner.  If the 
current user is an admin user or is a member of the Tool Shed’s Intergalactic 
Utilities Commission, all repositories will be created no matter the owner.  
Otherwise, only repositories whose associated owner is the current user will be 
created.

> 
> If so, would this mean a capsule can only be used one at import
> (but cannot be used to update a Tool Shed repository with a
> newer version of the source repository)?

Yes, currently the export / import features supports only the initial import 
into a different tool shed.  The feature has been introduced to streamline the 
Galaxy utility development process by providing an easier way to migrate a set 
of repositories from tool shed to tool shed.  Future enhancements to this 
feature will support updates to repositories.

> 
>>> I can see "Import repository capsule" as a new action at the
>>> bottom of the left hand column (under "Create new repository").
>>> 
>>> Is there an "Export repository capsule" entry somewhere?
>>> I can see a "Export this revision" action on each repository,
>>> is that it?
>>> 
>> 
>> Yes.
> 
> Would it make sense to rename it to "Export capsule for this revision"
> or something more explicit with the word "capsule" in the name?
> (I'm not sure how long these action names can be, but this is a
> little change which would help link the action to the corresponding
> ""Import repository capsule" menu.)

My current feature labels link the actions via the verbs ( export -> import ).  
The act of exporting a repository revision creates a capsule which can then be 
imported.  If more text is needed in the export label, the proper text should 
probably be: "Export this revision into a capsule".  I can certainly make that 
change if there is strong support for it.


> 
> Regards,
> 
> Peter
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