The latest galaxy build only allows importing workflows previously downloaded as files via URL. Can they be imported from a local directory instead of HTTP/FTP?
David Hoover Helix Systems Staff http://helix.nih.gov
The latest galaxy build only allows importing workflows previously downloaded as files via URL. Can they be imported from a local directory instead of HTTP/FTP?
Hi David,
Do you mean that you'd like to be able to import workflows as you can import datasets? What's the usage scenario that you imagine here?
Thanks, J.
On Sun, Nov 28, 2010 at 11:58 PM, Jeremy Goecks wrote:
The latest galaxy build only allows importing workflows previously downloaded as files via URL. Can they be imported from a local directory instead of HTTP/FTP?
Hi David,
Do you mean that you'd like to be able to import workflows as you can import datasets? What's the usage scenario that you imagine here?
Thanks, J.
I don't know what David has in mind, but I can imagine having a website with downloadable workflows, maybe one day as a bit of supplementary information. So giving the HTTP/FTP link to Galaxy could be useful. However, since workflow files are relatively small, downloading to your local computer then uploading to Galaxy isn't too onerous (but it is still two steps when it could be one).
I suppose it would be most useful when working on a slow internet connection (e.g. remote area) and/or you are using a locked down local computer (e.g. at an internet cafe, or a guest account at a conference) were you cannot save files to disk.
Peter
Huh? I would like to pull down a shared workflow for use on a local Galaxy instance. On the public Galaxy instance, click on 'Shared Data -> 'Published Workflows'. Choose any of the workflows and click 'Import workflow'. Now the workflow is in the user's personal history.
Click on 'Workflow' and find the newly imported workflow. Click on the workflow and choose 'Download or Export'. Now click 'Download workflow to file', and save the workflow on your local machine.
Here's the issue. The downloaded workflow file must be uploaded again to a shared HTTP/FTP site in order to be imported into the local Galaxy instance. Wouldn't it be much easier to simply upload the file from a local filesystem directly, rather than needing to re-export it to a shared FTP/HTTP area? The workflow files are not that big.
When you click on 'Upload or import workflow' from within the Workflow page, it only allows upload from a URL. Why can't it import from a local filesystem?
Our local Galaxy instance is available to users who do not have access to their own FTP/HTTP areas.
David
On Nov 29, 2010, at 4:23 AM, Peter Cock wrote:
On Sun, Nov 28, 2010 at 11:58 PM, Jeremy Goecks wrote:
The latest galaxy build only allows importing workflows previously downloaded as files via URL. Can they be imported from a local directory instead of HTTP/FTP?
Hi David,
Do you mean that you'd like to be able to import workflows as you can import datasets? What's the usage scenario that you imagine here?
Thanks, J.
I don't know what David has in mind, but I can imagine having a website with downloadable workflows, maybe one day as a bit of supplementary information. So giving the HTTP/FTP link to Galaxy could be useful. However, since workflow files are relatively small, downloading to your local computer then uploading to Galaxy isn't too onerous (but it is still two steps when it could be one).
I suppose it would be most useful when working on a slow internet connection (e.g. remote area) and/or you are using a locked down local computer (e.g. at an internet cafe, or a guest account at a conference) were you cannot save files to disk.
Peter
I can understand the confusion. We'll probably eventually add an 'upload from local file' option, but in the meantime, Galaxy's current functionality enables you to complete the scenario you describe.
To import a workflow from a file, open the downloaded workflow file in your favorite text editor, copy the file's contents into the box labeled 'Encoded workflow', and click 'Import.'
Thanks, J.
On Nov 29, 2010, at 8:33 AM, David Hoover wrote:
Huh? I would like to pull down a shared workflow for use on a local Galaxy instance. On the public Galaxy instance, click on 'Shared Data -> 'Published Workflows'. Choose any of the workflows and click 'Import workflow'. Now the workflow is in the user's personal history.
Click on 'Workflow' and find the newly imported workflow. Click on the workflow and choose 'Download or Export'. Now click 'Download workflow to file', and save the workflow on your local machine.
Here's the issue. The downloaded workflow file must be uploaded again to a shared HTTP/FTP site in order to be imported into the local Galaxy instance. Wouldn't it be much easier to simply upload the file from a local filesystem directly, rather than needing to re-export it to a shared FTP/HTTP area? The workflow files are not that big.
When you click on 'Upload or import workflow' from within the Workflow page, it only allows upload from a URL. Why can't it import from a local filesystem?
Our local Galaxy instance is available to users who do not have access to their own FTP/HTTP areas.
David
On Nov 29, 2010, at 4:23 AM, Peter Cock wrote:
On Sun, Nov 28, 2010 at 11:58 PM, Jeremy Goecks wrote:
The latest galaxy build only allows importing workflows previously downloaded as files via URL. Can they be imported from a local directory instead of HTTP/FTP?
Hi David,
Do you mean that you'd like to be able to import workflows as you can import datasets? What's the usage scenario that you imagine here?
Thanks, J.
I don't know what David has in mind, but I can imagine having a website with downloadable workflows, maybe one day as a bit of supplementary information. So giving the HTTP/FTP link to Galaxy could be useful. However, since workflow files are relatively small, downloading to your local computer then uploading to Galaxy isn't too onerous (but it is still two steps when it could be one).
I suppose it would be most useful when working on a slow internet connection (e.g. remote area) and/or you are using a locked down local computer (e.g. at an internet cafe, or a guest account at a conference) were you cannot save files to disk.
Peter
J.
This changeset makes it easier to move Galaxy workflows from one instance to another without needing to download it:
http://bitbucket.org/galaxy/galaxy-central/changeset/6774eff6454b
The gist is that a user can now get a URL from one Galaxy instance and paste it into the 'Import Workflow' form of another Galaxy instance to import a workflow from the first Galaxy instance.
J. On Nov 29, 2010, at 10:00 AM, Jeremy Goecks wrote:
I can understand the confusion. We'll probably eventually add an 'upload from local file' option, but in the meantime, Galaxy's current functionality enables you to complete the scenario you describe.
To import a workflow from a file, open the downloaded workflow file in your favorite text editor, copy the file's contents into the box labeled 'Encoded workflow', and click 'Import.'
Thanks, J.
On Nov 29, 2010, at 8:33 AM, David Hoover wrote:
Huh? I would like to pull down a shared workflow for use on a local Galaxy instance. On the public Galaxy instance, click on 'Shared Data -> 'Published Workflows'. Choose any of the workflows and click 'Import workflow'. Now the workflow is in the user's personal history.
Click on 'Workflow' and find the newly imported workflow. Click on the workflow and choose 'Download or Export'. Now click 'Download workflow to file', and save the workflow on your local machine.
Here's the issue. The downloaded workflow file must be uploaded again to a shared HTTP/FTP site in order to be imported into the local Galaxy instance. Wouldn't it be much easier to simply upload the file from a local filesystem directly, rather than needing to re-export it to a shared FTP/HTTP area? The workflow files are not that big.
When you click on 'Upload or import workflow' from within the Workflow page, it only allows upload from a URL. Why can't it import from a local filesystem?
Our local Galaxy instance is available to users who do not have access to their own FTP/HTTP areas.
David
On Nov 29, 2010, at 4:23 AM, Peter Cock wrote:
On Sun, Nov 28, 2010 at 11:58 PM, Jeremy Goecks wrote:
The latest galaxy build only allows importing workflows previously downloaded as files via URL. Can they be imported from a local directory instead of HTTP/FTP?
Hi David,
Do you mean that you'd like to be able to import workflows as you can import datasets? What's the usage scenario that you imagine here?
Thanks, J.
I don't know what David has in mind, but I can imagine having a website with downloadable workflows, maybe one day as a bit of supplementary information. So giving the HTTP/FTP link to Galaxy could be useful. However, since workflow files are relatively small, downloading to your local computer then uploading to Galaxy isn't too onerous (but it is still two steps when it could be one).
I suppose it would be most useful when working on a slow internet connection (e.g. remote area) and/or you are using a locked down local computer (e.g. at an internet cafe, or a guest account at a conference) were you cannot save files to disk.
Peter
J.
J.
galaxy-dev@lists.galaxyproject.org
-
David Hoover -
Jeremy Goecks -
Peter Cock