Is anyone using composite datatype uploads?
Hello everyone, We are considering to disable the deprecated upload tool form which is currently accessible through Tool panel > Get Data > Upload file. The new upload feature (icon at the top of the Tool panel) covers all of its functionality except uploading composite datatypes like e.g. Velvet. Please let us know if you are using the composite file upload functionality of the former tool form. Thanks, Sam
Well there is at least one person using this functionality - http://dev.list.galaxyproject.org/Problem-to-upload-data-to-Galaxy-when-usin.... Just to make this more concrete - Sam has swapped the "upload file" button to use the new upload widget this release cycle (targeted for December 1st). So barring negative feedback - uploading pbed or velvet report datatypes (or other similar composite datatypes) will no longer be possible via the GUI. -John On Thu, Aug 14, 2014 at 2:32 PM, Aysam Guerler <aysam.guerler@gmail.com> wrote:
Hello everyone,
We are considering to disable the deprecated upload tool form which is currently accessible through Tool panel > Get Data > Upload file. The new upload feature (icon at the top of the Tool panel) covers all of its functionality except uploading composite datatypes like e.g. Velvet.
Please let us know if you are using the composite file upload functionality of the former tool form.
Thanks, Sam
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Hi John, Sam, I've not done it yet, but was hoping to implement uploading of BLAST databases at some point - mainly for use within the test framework, rather than expecting it to be useful for the end user. Is the issue here uploading an archive (e.g. .zip or .tar.gz) or offering a way to pick multiple files to be treated together as a composite dataset? Peter On Wed, Nov 19, 2014 at 3:32 PM, John Chilton <jmchilton@gmail.com> wrote:
Well there is at least one person using this functionality - http://dev.list.galaxyproject.org/Problem-to-upload-data-to-Galaxy-when-usin....
Just to make this more concrete - Sam has swapped the "upload file" button to use the new upload widget this release cycle (targeted for December 1st). So barring negative feedback - uploading pbed or velvet report datatypes (or other similar composite datatypes) will no longer be possible via the GUI.
-John
On Thu, Aug 14, 2014 at 2:32 PM, Aysam Guerler <aysam.guerler@gmail.com> wrote:
Hello everyone,
We are considering to disable the deprecated upload tool form which is currently accessible through Tool panel > Get Data > Upload file. The new upload feature (icon at the top of the Tool panel) covers all of its functionality except uploading composite datatypes like e.g. Velvet.
Please let us know if you are using the composite file upload functionality of the former tool form.
Thanks, Sam
___________________________________________________________ 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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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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What is disappearing (sortof) is the UI for selecting the individual pieces - I don't think anything in the API has changed yet. I don't think datatypes have a way of picking apart an archive file for their pieces - but it would make a lot of sense to implement. Total Aside: I wonder if testing tools one at a time is always the best approach - one can imagine (for instance in your indexer's case) utility in being able to string together some pre-steps or post-steps for things like conversions to ease testing. For some very yak-shavey reasons I wrote a little YAML DSL (https://gist.github.com/jmchilton/3b66f101c53c6734d3c5) for building Galaxy workflows to test some tool and workflow features. I have been considering extending it with the ability to specify input and outputs conditions and adding it to planemo to test repositories . (By assigning labels at a level above the actual RAW workflow - it solves the biggest problem that was present with the workflow testing stuff we briefly discussed last winder). It would be cool for local and CI testing - but it is more difficult to see how that pattern could work with the tool shed test framework where the ids are not simple and the tools may be split across many repositories.</aside> -John On Wed, Nov 19, 2014 at 10:39 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi John, Sam,
I've not done it yet, but was hoping to implement uploading of BLAST databases at some point - mainly for use within the test framework, rather than expecting it to be useful for the end user.
Is the issue here uploading an archive (e.g. .zip or .tar.gz) or offering a way to pick multiple files to be treated together as a composite dataset?
Peter
On Wed, Nov 19, 2014 at 3:32 PM, John Chilton <jmchilton@gmail.com> wrote:
Well there is at least one person using this functionality - http://dev.list.galaxyproject.org/Problem-to-upload-data-to-Galaxy-when-usin....
Just to make this more concrete - Sam has swapped the "upload file" button to use the new upload widget this release cycle (targeted for December 1st). So barring negative feedback - uploading pbed or velvet report datatypes (or other similar composite datatypes) will no longer be possible via the GUI.
-John
On Thu, Aug 14, 2014 at 2:32 PM, Aysam Guerler <aysam.guerler@gmail.com> wrote:
Hello everyone,
We are considering to disable the deprecated upload tool form which is currently accessible through Tool panel > Get Data > Upload file. The new upload feature (icon at the top of the Tool panel) covers all of its functionality except uploading composite datatypes like e.g. Velvet.
Please let us know if you are using the composite file upload functionality of the former tool form.
Thanks, Sam
___________________________________________________________ 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/
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/
participants (3)
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Aysam Guerler -
John Chilton -
Peter Cock