User: sfischer

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sfischer30
Reputation:
30
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New User
Location:
United States
Last seen:
2 years, 1 month ago
Joined:
3 years, 4 months ago
Email:
s*******@upenn.edu

Posts by sfischer

<prev • 8 results • page 1 of 1 • next >
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REST API - a small bug in jobs endpoint
... This is a minor bug, easily worked around.   But, I thought I should still report it. When i call this endpoint: https://usegalaxy.org/api/jobs/bbd44e69cb8906b508c63628260d9ebe part of the JSON returned describes the param values used: "params": { "__workflow_invocation_uuid__": "\"8f68ffc68 ...
api written 2.2 years ago by sfischer30 • updated 2.2 years ago by Dannon Baker3.7k
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Comment: C: REST API - can't find workflow step_id in a workflow invocation
... Hi Dannon, I have been prototyping on usegalaxy.org.   You're right we will soon have our own instance running. While we wait for this to be fixed in the stable branch, can you provide a patch we can apply to our (upcoming) instance?  Just let me know what file to edit, and what the change would b ...
written 2.2 years ago by sfischer30
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Comment: C: REST API - can't find workflow step_id in a workflow invocation
... Dannon, Thanks. It looks like this workaround isn't going to work for me: 1) i am operating remotely, so cannot import that code. (i am running my code, via REST, against usegalaxy.org) 2) i tried this in perl, locally: % perl -e 'use Crypt::Blowfish; my $c = new Crypt::Blowfish "USING THE DEF ...
written 2.2 years ago by sfischer30
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Answer: A: REST API - can't find workflow step_id in a workflow invocation
... Dannon, Thanks very much. I had a guess that was it, but couldn't find it in the code base. I do think it would be good, as you suggest, for galaxy to encode this value in the workflow info returned by the API call, to make it consistent with the invocation. In the meantime, I can try the workaro ...
written 2.2 years ago by sfischer30
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REST API - can't find workflow step_id in a workflow invocation
... Hi, i am using the REST API for workflows, as documented here: https://galaxy.readthedocs.org/en/master/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.workflows I need to: GET a workflow invocation scrape its parameter values fire off a new run of that workflow based on ...
api written 2.2 years ago by sfischer30
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Answer: A: workflow API problem
... OK, sorry.  I figured it out.  It is a typo in the API Documentation.  http://galaxy-dist.readthedocs.org/en/latest/lib/galaxy.webapps.galaxy.api.html#module-galaxy.webapps.galaxy.api.workflows The doc says: GET /api/workflows/{workflow_id}/invocation/{invocation_id} but should say: GET /api/wo ...
written 2.5 years ago by sfischer30 • updated 2.5 years ago by Dannon Baker3.7k
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workflow API problem
... Hi, I issue this call to the API: https://usegalaxy.org/api/workflows/ba06423ff18d37cc/invocations?key=REDACTED and get this response: [ { "update_time": "2015-08-06T11:51:49.365687", "uuid": "665407a8-3c31-11e5-bd2a-005056a52a46", "history_id": "148c3a937daeb25d", "state": "s ...
api workflow written 2.5 years ago by sfischer30 • updated 2.5 years ago by Dannon Baker3.7k
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Can Trackster be used stand-alone?
... Hi, We are evaluating Genome Browsers to be embedded in our functional genomics website.  We are currently using GBrowse, but it is getting long in the tooth.  Others we are looking at are JBrowse and BioDalliance. Is Trackster available for stand-alone installation, without a galaxy instance?  Is ...
stand-alone trackster embed written 3.3 years ago by sfischer30 • updated 3.3 years ago by Jeremy Goecks50

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