Exporting & Importing Tool Shed repository is just great!
Hi Tool Shed Team! I know I'm always finding bugs and keeping you busy, but this mail is different! The Tool Shed exporting and importing feature is just great, its save so much time and is a pleasure to use. Everyone should try it! So thanks for the hard work you all put into the Tool Shed over the last month. I really enjoy to put my tools into it! Thanks, Bjoern
Many thanks, Björn for your very kind words. The Tool Shed would not be what it is without your hard work as well. We hoped the export/import capsule feature would be beneficial, so it's great to hear confirmation that it is. Also, please don't hesitate to continue to contact us with newly discovered issues! Greg Von Kuster On Mar 3, 2014, at 12:02 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Tool Shed Team!
I know I'm always finding bugs and keeping you busy, but this mail is different! The Tool Shed exporting and importing feature is just great, its save so much time and is a pleasure to use. Everyone should try it! So thanks for the hard work you all put into the Tool Shed over the last month. I really enjoy to put my tools into it!
Thanks, Bjoern ___________________________________________________________ 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/
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Hi Guys, Is this stuff on the wiki? 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)? 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? Thanks, Peter On Mon, Mar 3, 2014 at 5:58 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Many thanks, Björn for your very kind words. The Tool Shed would not be what it is without your hard work as well. We hoped the export/import capsule feature would be beneficial, so it's great to hear confirmation that it is. Also, please don't hesitate to continue to contact us with newly discovered issues!
Greg Von Kuster
On Mar 3, 2014, at 12:02 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Tool Shed Team!
I know I'm always finding bugs and keeping you busy, but this mail is different! The Tool Shed exporting and importing feature is just great, its save so much time and is a pleasure to use. Everyone should try it! So thanks for the hard work you all put into the Tool Shed over the last month. I really enjoy to put my tools into it!
Thanks, Bjoern
On Mar 3, 2014, at 1:13 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Guys,
Is this stuff on the wiki?
Not completely yet.
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.
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.
Thanks,
Peter
On Mon, Mar 3, 2014 at 5:58 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Many thanks, Björn for your very kind words. The Tool Shed would not be what it is without your hard work as well. We hoped the export/import capsule feature would be beneficial, so it's great to hear confirmation that it is. Also, please don't hesitate to continue to contact us with newly discovered issues!
Greg Von Kuster
On Mar 3, 2014, at 12:02 PM, Björn Grüning <bjoern.gruening@gmail.com> wrote:
Hi Tool Shed Team!
I know I'm always finding bugs and keeping you busy, but this mail is different! The Tool Shed exporting and importing feature is just great, its save so much time and is a pleasure to use. Everyone should try it! So thanks for the hard work you all put into the Tool Shed over the last month. I really enjoy to put my tools into it!
Thanks, Bjoern
On Mon, Mar 3, 2014 at 6:33 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
On Mar 3, 2014, at 1:13 PM, Peter Cock <p.j.a.cock@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
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? 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)?
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.) Regards, Peter
Hi Peter, On Mar 4, 2014, at 5:19 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Mar 3, 2014 at 6:33 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
On Mar 3, 2014, at 1:13 PM, Peter Cock <p.j.a.cock@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 ___________________________________________________________ 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/
On Tue, Mar 4, 2014 at 2:38 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Peter, On Mar 4, 2014, at 5:19 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Mar 3, 2014 at 6:33 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
On Mar 3, 2014, at 1:13 PM, Peter Cock <p.j.a.cock@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/
I thought I'd already subscribed to your blog, but evidently hadn't (or there was a glitch). Done now :) I would however very much like to see at least a stub entry on the wiki about the import/export of capsules (linking to the blog) so it can be found by searching the wiki. Peter
participants (3)
-
Björn Grüning -
Greg Von Kuster -
Peter Cock