Hello,
Is it possible to let a tool in a workflow manage the users history? For instance, I have a tool that takes a variable number of user-uploaded CSV files as input and merges them into one file. Before running this tool, the user thus has a number of CSV files in the history which I would like to 'replace' with the single merged file. I was hoping that when I remove a file from disk that it would also be removed from the history, but that only results in a 'The resource could not be found.' error. Alternatively, is it possible to create a composite datafile/history item from uploaded files? In any case, I would like to remove the separately uploaded files from the users history which makes selecting files for the next step(s) easier.
(this is a bit of a followup for: http://gmod.827538.n3.nabble.com/Creating-new-datatype-with-variable-number-...)
One other question, is there (any) documentation available on the Galaxy API or a set of example files?
Thanks for your input!
Regards,
Marcel.
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Marcel,
It isn't currently possible to delete datasets from within workflows. If I'm understanding your situation correctly, to simplify the view of a history after running a workflow, you could use the workflow output toggle (the asterisk next to each output in the workflow editor view) and select only the particular outputs you actually want to see. The rest of the outputs are still in the destination history, but hidden from view by default. This won't help you with disk space, though, so you might also want to use the new functionality available for placing the results of a workflow in a new history to accomplish what you want, deleting the previous history that was cluttered with inputs after the workflow has run.
Regarding the Galaxy API, you can look at the README file in the scripts/api/ directory of your galaxy installation (also at https://bitbucket.org/galaxy/galaxy-central/src/76c18b38a3b8/scripts/api/REA...) for a some examples and hints to get you started. More detailed documentation should be available soon though.
-Dannon
On Jan 20, 2011, at 4:15 AM, Kempenaar, M (med) wrote:
Hello,
Is it possible to let a tool in a workflow manage the users history? For instance, I have a tool that takes a variable number of user-uploaded CSV files as input and merges them into one file. Before running this tool, the user thus has a number of CSV files in the history which I would like to 'replace' with the single merged file. I was hoping that when I remove a file from disk that it would also be removed from the history, but that only results in a 'The resource could not be found.' error. Alternatively, is it possible to create a composite datafile/history item from uploaded files? In any case, I would like to remove the separately uploaded files from the users history which makes selecting files for the next step(s) easier.
(this is a bit of a followup for: http://gmod.827538.n3.nabble.com/Creating-new-datatype-with-variable-number-...)
One other question, is there (any) documentation available on the Galaxy API or a set of example files?
Thanks for your input!
Regards,
Marcel.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
i'm resurrecting this thread to see if there's any more support for the idea of deleting intermediate files in a workflow. i think this is an important feature to have. oftentimes a workflow creates many intermediate files no one will ever look at. and leaving it up to the user to cleanup their data files is asking too much. there's another ticket regarding allow users to still be able to preview the metadata of deleted workflow history items and together these would go together nicely.
On Wed, Jan 26, 2011 at 1:36 PM, Dannon Baker dannonbaker@me.com wrote:
Marcel,
It isn't currently possible to delete datasets from within workflows. If I'm understanding your situation correctly, to simplify the view of a history after running a workflow, you could use the workflow output toggle (the asterisk next to each output in the workflow editor view) and select only the particular outputs you actually want to see. The rest of the outputs are still in the destination history, but hidden from view by default. This won't help you with disk space, though, so you might also want to use the new functionality available for placing the results of a workflow in a new history to accomplish what you want, deleting the previous history that was cluttered with inputs after the workflow has run.
Regarding the Galaxy API, you can look at the README file in the scripts/api/ directory of your galaxy installation (also at https://bitbucket.org/galaxy/galaxy-central/src/76c18b38a3b8/scripts/api/REA...) for a some examples and hints to get you started. More detailed documentation should be available soon though.
-Dannon
On Jan 20, 2011, at 4:15 AM, Kempenaar, M (med) wrote:
Hello,
Is it possible to let a tool in a workflow manage the users history? For
instance, I have a tool that takes a variable number of user-uploaded CSV files as input and merges them into one file. Before running this tool, the user thus has a number of CSV files in the history which I would like to 'replace' with the single merged file.
I was hoping that when I remove a file from disk that it would also be
removed from the history, but that only results in a 'The resource could not be found.' error.
Alternatively, is it possible to create a composite datafile/history item
from uploaded files? In any case, I would like to remove the separately uploaded files from the users history which makes selecting files for the next step(s) easier.
(this is a bit of a followup for:
http://gmod.827538.n3.nabble.com/Creating-new-datatype-with-variable-number-... )
One other question, is there (any) documentation available on the Galaxy
API or a set of example files?
Thanks for your input!
Regards,
Marcel.
De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de
geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht.
The contents of this message are confidential and only intended for the
eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
On Sep 7, 2011, at 8:10 PM, Edward Kirton wrote:
i'm resurrecting this thread to see if there's any more support for the idea of deleting intermediate files in a workflow. i think this is an important feature to have. oftentimes a workflow creates many intermediate files no one will ever look at. and leaving it up to the user to cleanup their data files is asking too much. there's another ticket regarding allow users to still be able to preview the metadata of deleted workflow history items and together these would go together nicely.
I am _very_ interested in this feature
-- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153
I haven't had a chance to do anything on this yet, but I'll see if I can work something out in the near future.
-Dannon
On Sep 7, 2011, at 9:34 PM, Glen Beane wrote:
On Sep 7, 2011, at 8:10 PM, Edward Kirton wrote:
i'm resurrecting this thread to see if there's any more support for the idea of deleting intermediate files in a workflow. i think this is an important feature to have. oftentimes a workflow creates many intermediate files no one will ever look at. and leaving it up to the user to cleanup their data files is asking too much. there's another ticket regarding allow users to still be able to preview the metadata of deleted workflow history items and together these would go together nicely.
I am _very_ interested in this feature
-- Glen L. Beane Senior Software Engineer The Jackson Laboratory (207) 288-6153
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Kempenaar, M (med)