Visualise Galaxy workflows using graphviz
Hi there Because my Galaxy workflows tend to sprawl outside the viewable space in my browser, I've written a script that, when given a workflow JSON file as input, writes out a graphviz dot format graph of the workflow. By default the graph treats datasets as nodes and analyses as edges (unlike the Galaxy workflow editor, but quite like the way the history is presented), but you can choose to have analyses as nodes (and thus datasets as edges) too. In case anyone else finds this useful, the code can be downloaded from my bitbucket: https://bitbucket.org/pvanheus/galaxy/src/f29453f3d9d8/contrib/workflow_to_d... Usage is something like: ./workflow_to_dot.py Galaxy-Workflow.ga |dot -Tsvg >workflow.svg and then you can view your workflow.svg with eog or another viewer. Peter
Thanks for sharing Peter. FWIW, there is already code in Galaxy to generate SVG from a workflow. See the gen_image function in web/controllers/workflow.py I think this code is used when workflows are included in the tool shed as well. If your code is better in some way(s), please consider a pull request. It should be fairly straightforward to add an option to a workflow's menu to generate SVG for it. Best, J. On May 23, 2012, at 4:44 PM, Peter van Heusden wrote:
Hi there
Because my Galaxy workflows tend to sprawl outside the viewable space in my browser, I've written a script that, when given a workflow JSON file as input, writes out a graphviz dot format graph of the workflow. By default the graph treats datasets as nodes and analyses as edges (unlike the Galaxy workflow editor, but quite like the way the history is presented), but you can choose to have analyses as nodes (and thus datasets as edges) too.
In case anyone else finds this useful, the code can be downloaded from my bitbucket:
https://bitbucket.org/pvanheus/galaxy/src/f29453f3d9d8/contrib/workflow_to_d...
Usage is something like:
./workflow_to_dot.py Galaxy-Workflow.ga |dot -Tsvg >workflow.svg
and then you can view your workflow.svg with eog or another viewer.
Peter
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Hi, please find attached a small patch that add the gen_image() functionality to the export-workflow UI. I was not able to figure out how to add a patch to the trello card. But at least i created one ;). https://trello.com/c/PGz7JNzO Ciao, Bjoern
Thanks for sharing Peter.
FWIW, there is already code in Galaxy to generate SVG from a workflow. See the gen_image function in web/controllers/workflow.py I think this code is used when workflows are included in the tool shed as well.
If your code is better in some way(s), please consider a pull request. It should be fairly straightforward to add an option to a workflow's menu to generate SVG for it.
Best, J.
On May 23, 2012, at 4:44 PM, Peter van Heusden wrote:
Hi there
Because my Galaxy workflows tend to sprawl outside the viewable space in my browser, I've written a script that, when given a workflow JSON file as input, writes out a graphviz dot format graph of the workflow. By default the graph treats datasets as nodes and analyses as edges (unlike the Galaxy workflow editor, but quite like the way the history is presented), but you can choose to have analyses as nodes (and thus datasets as edges) too.
In case anyone else finds this useful, the code can be downloaded from my bitbucket:
https://bitbucket.org/pvanheus/galaxy/src/f29453f3d9d8/contrib/workflow_to_d...
Usage is something like:
./workflow_to_dot.py Galaxy-Workflow.ga |dot -Tsvg >workflow.svg
and then you can view your workflow.svg with eog or another viewer.
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:
___________________________________________________________ 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:
please find attached a small patch that add the gen_image() functionality to the export-workflow UI.
Thanks for the contribution. I committed a modified version of it: https://bitbucket.org/galaxy/galaxy-central/commits/0e064a23864c846483b35f89... Specifically, I (a) used gen_image directly rather than a wrapper method and (b) added the code to workflow's export template rather than the base template.
I was not able to figure out how to add a patch to the trello card. But at least i created one ;).
This isn't possible as best I know. Pull requests are the (highly) preferred way to contribute code to the project. Best, J.
participants (3)
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Björn Grüning -
Jeremy Goecks -
Peter van Heusden