Tool Shed Problem
Hi Galaxy team, I created a new repository on the tool shed called "test", I wanted to see what steps were required to publish a tool before I go ahead and release the production version. I then tried to change the name of the repository and got a server error. When I search for test, try to navigate to 2nd page of the repository list or view my own repositories the server error occurs. Apologies if I broke it... On a side note, I did not see an option to delete a created repository. Also, my test repository went live straight away. Would it make sense to be able to create a repository and load files then have a publish button for when you choose to release. Thanks Shaun -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
Hello Shaun, On Jul 12, 2011, at 6:07 AM, SHAUN WEBB wrote:
Hi Galaxy team,
I created a new repository on the tool shed called "test", I wanted to see what steps were required to publish a tool before I go ahead and release the production version. I then tried to change the name of the repository and got a server error.
This problem was due to a bug which I've fixed, so the tool shed is functional with your renamed repository. Thanks for finding the bug...
When I search for test, try to navigate to 2nd page of the repository list or view my own repositories the server error occurs.
Apologies if I broke it...
You didn't , sorry for the bug!
On a side note, I did not see an option to delete a created repository.
Yes, currently only a tool shed admin ( me ) can delete a repository. I've considered allowing owners to delete repositories, but that may open up problems with users that want to be able to download tools from that repository because they have downloaded them in the past. Obviously this issue affects the "reproducibility factor". We'll have to figure out how to handle this optimally...
Also, my test repository went live straight away. Would it make sense to be able to create a repository and load files then have a publish button for when you choose to release.
I'm not sure I understand the issue here. Why do you feel that it is important to have this extra step? Is it just that repositories should not be displayed until they contain files? if so, I can probably make that change, and it won't require clicking a "Publish" button.
Thanks Shaun
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Shaun, I forgot to mention, if you want to just fool around with tool shed features, check out the test version of the tool shed at http://testtoolshed.g2.bx.psu.edu/ On Jul 12, 2011, at 10:24 AM, Greg Von Kuster wrote:
Hello Shaun,
On Jul 12, 2011, at 6:07 AM, SHAUN WEBB wrote:
Hi Galaxy team,
I created a new repository on the tool shed called "test", I wanted to see what steps were required to publish a tool before I go ahead and release the production version. I then tried to change the name of the repository and got a server error.
This problem was due to a bug which I've fixed, so the tool shed is functional with your renamed repository. Thanks for finding the bug...
When I search for test, try to navigate to 2nd page of the repository list or view my own repositories the server error occurs.
Apologies if I broke it...
You didn't , sorry for the bug!
On a side note, I did not see an option to delete a created repository.
Yes, currently only a tool shed admin ( me ) can delete a repository. I've considered allowing owners to delete repositories, but that may open up problems with users that want to be able to download tools from that repository because they have downloaded them in the past. Obviously this issue affects the "reproducibility factor". We'll have to figure out how to handle this optimally...
Also, my test repository went live straight away. Would it make sense to be able to create a repository and load files then have a publish button for when you choose to release.
I'm not sure I understand the issue here. Why do you feel that it is important to have this extra step? Is it just that repositories should not be displayed until they contain files? if so, I can probably make that change, and it won't require clicking a "Publish" button.
Thanks Shaun
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Thanks Greg, could you delete the repository I created please? I guess that step isn't necessary as most people won't create repositories until they are ready to go. It would stop curious users like me creating empty repositories by just clicking buttons.. Is there more documentation on what is required to publish a new tool in the tool shed? Shaun Quoting Greg Von Kuster <greg@bx.psu.edu> on Tue, 12 Jul 2011 10:24:28 -0400:
Hello Shaun,
On Jul 12, 2011, at 6:07 AM, SHAUN WEBB wrote:
Hi Galaxy team,
I created a new repository on the tool shed called "test", I wanted to see what steps were required to publish a tool before I go ahead and release the production version. I then tried to change the name of the repository and got a server error.
This problem was due to a bug which I've fixed, so the tool shed is functional with your renamed repository. Thanks for finding the bug...
When I search for test, try to navigate to 2nd page of the repository list or view my own repositories the server error occurs.
Apologies if I broke it...
You didn't , sorry for the bug!
On a side note, I did not see an option to delete a created repository.
Yes, currently only a tool shed admin ( me ) can delete a repository. I've considered allowing owners to delete repositories, but that may open up problems with users that want to be able to download tools from that repository because they have downloaded them in the past. Obviously this issue affects the "reproducibility factor". We'll have to figure out how to handle this optimally...
Also, my test repository went live straight away. Would it make sense to be able to create a repository and load files then have a publish button for when you choose to release.
I'm not sure I understand the issue here. Why do you feel that it is important to have this extra step? Is it just that repositories should not be displayed until they contain files? if so, I can probably make that change, and it won't require clicking a "Publish" button.
Thanks Shaun
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
On Jul 12, 2011, at 11:54 AM, SHAUN WEBB wrote:
Thanks Greg, could you delete the repository I created please?
Are you eventually going to use your repository? If you are planning to never upload a tool, I'll delete it. Otherwise, I'll leave it active so you can eventually use it.
I guess that step isn't necessary as most people won't create repositories until they are ready to go. It would stop curious users like me creating empty repositories by just clicking buttons..
Is there more documentation on what is required to publish a new tool in the tool shed?
Nothing yet, but as time permits, there will be. It's basically just common sense. If you have developed a tool that you feel is useful, upload it. Additional things like including working functional tests with small input / output datasets makes it even more useful. A very important feature that I recently added is baseline functionality for repository metadata. An attempt is made to generate repository metadata with each new change set. If the attempt is not successful, metadata is not generated for that change set. This metadata will eventually be an important ingredient in allowing the tool to be automatically installed from the tool shed into a Galaxy instance with just a few mouse clicks.
Shaun
Quoting Greg Von Kuster <greg@bx.psu.edu> on Tue, 12 Jul 2011 10:24:28 -0400:
Hello Shaun,
On Jul 12, 2011, at 6:07 AM, SHAUN WEBB wrote:
Hi Galaxy team,
I created a new repository on the tool shed called "test", I wanted to see what steps were required to publish a tool before I go ahead and release the production version. I then tried to change the name of the repository and got a server error.
This problem was due to a bug which I've fixed, so the tool shed is functional with your renamed repository. Thanks for finding the bug...
When I search for test, try to navigate to 2nd page of the repository list or view my own repositories the server error occurs.
Apologies if I broke it...
You didn't , sorry for the bug!
On a side note, I did not see an option to delete a created repository.
Yes, currently only a tool shed admin ( me ) can delete a repository. I've considered allowing owners to delete repositories, but that may open up problems with users that want to be able to download tools from that repository because they have downloaded them in the past. Obviously this issue affects the "reproducibility factor". We'll have to figure out how to handle this optimally...
Also, my test repository went live straight away. Would it make sense to be able to create a repository and load files then have a publish button for when you choose to release.
I'm not sure I understand the issue here. Why do you feel that it is important to have this extra step? Is it just that repositories should not be displayed until they contain files? if so, I can probably make that change, and it won't require clicking a "Publish" button.
Thanks Shaun
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
I am, but I would like to be able to change the category. It will be an RNA-seq tool. Shaun Quoting Greg Von Kuster <greg@bx.psu.edu> on Tue, 12 Jul 2011 12:38:08 -0400:
On Jul 12, 2011, at 11:54 AM, SHAUN WEBB wrote:
Thanks Greg, could you delete the repository I created please?
Are you eventually going to use your repository? If you are planning to never upload a tool, I'll delete it. Otherwise, I'll leave it active so you can eventually use it.
I guess that step isn't necessary as most people won't create repositories until they are ready to go. It would stop curious users like me creating empty repositories by just clicking buttons..
Is there more documentation on what is required to publish a new tool in the tool shed?
Nothing yet, but as time permits, there will be. It's basically just common sense. If you have developed a tool that you feel is useful, upload it. Additional things like including working functional tests with small input / output datasets makes it even more useful.
A very important feature that I recently added is baseline functionality for repository metadata. An attempt is made to generate repository metadata with each new change set. If the attempt is not successful, metadata is not generated for that change set. This metadata will eventually be an important ingredient in allowing the tool to be automatically installed from the tool shed into a Galaxy instance with just a few mouse clicks.
Shaun
Quoting Greg Von Kuster <greg@bx.psu.edu> on Tue, 12 Jul 2011 10:24:28 -0400:
Hello Shaun,
On Jul 12, 2011, at 6:07 AM, SHAUN WEBB wrote:
Hi Galaxy team,
I created a new repository on the tool shed called "test", I wanted to see what steps were required to publish a tool before I go ahead and release the production version. I then tried to change the name of the repository and got a server error.
This problem was due to a bug which I've fixed, so the tool shed is functional with your renamed repository. Thanks for finding the bug...
When I search for test, try to navigate to 2nd page of the repository list or view my own repositories the server error occurs.
Apologies if I broke it...
You didn't , sorry for the bug!
On a side note, I did not see an option to delete a created repository.
Yes, currently only a tool shed admin ( me ) can delete a repository. I've considered allowing owners to delete repositories, but that may open up problems with users that want to be able to download tools from that repository because they have downloaded them in the past. Obviously this issue affects the "reproducibility factor". We'll have to figure out how to handle this optimally...
Also, my test repository went live straight away. Would it make sense to be able to create a repository and load files then have a publish button for when you choose to release.
I'm not sure I understand the issue here. Why do you feel that it is important to have this extra step? Is it just that repositories should not be displayed until they contain files? if so, I can probably make that change, and it won't require clicking a "Publish" button.
Thanks Shaun
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
___________________________________________________________ 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:
Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
participants (2)
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Greg Von Kuster -
SHAUN WEBB