User: mrals89

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mrals8950
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2 years, 5 months ago
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Posts by mrals89

<prev • 20 results • page 1 of 2 • next >
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[Tool Config] How to enforce cleanup tasks (shell commands) on job cancelation
... Hello, I have a tool which submits a custom pipeline shell script to our SGE. When a user cancels these jobs in Galaxy, the SGE jobs persist. Are there any "cleanup" tags for the XML that can perform certain shell commands before the job is considered canceled? Thank you! ...
xml galaxy tool-config tool written 2.5 years ago by mrals8950 • updated 2.3 years ago by jmchilton1.0k
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How do I build a Galaxy/Cloudman AMI starting from my corporate AMI?
... Hi everyone, I would like to build my own Cloudman AMI; I work for a company that has security protocols which require that I build my own image from our corporate "blessed" AMI. Are there any scripts, Dockerfiles, or guides for creating a Cloudman AMI? I figured this was a good place to start... ...
galaxy cloudman aws amazon ami written 2.6 years ago by mrals8950 • updated 2.6 years ago by Enis Afgan670
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Comment: C: Help New Cloud Cluster Key ID and Secret Key!!!
... Hi Ana, I am having the same issue with no luck figuring out the issue. Does your AWS IAM user by any chance have admin privileges? ...
written 2.8 years ago by mrals8950
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Comment: C: Internal Server Error: Galaxy was unable to successfully complete your request
... Has there been any update on this? I'm getting the same issue. ...
written 2.8 years ago by mrals8950
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Comment: C: Documentation for <collection> tag?
... ..Thank you! ...
written 2.8 years ago by mrals8950
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Comment: C: Documentation for <collection> tag?
... Gladly! That presentation was actually how I learned that collections were possible in tool configuration within galaxy. The tool subsamples paired-end fastq files, such that randomly selected mates are always kept or removed together. This requires paired->paired mapping, and often would occur o ...
written 2.8 years ago by mrals8950
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Comment: C: Documentation for <collection> tag?
... Yes, you're absolutely right. However, I didn't have an example to use to demonstrate this "implicit mapping" functionality. Is this documented anywhere? After a few hours of exploring, I figured out that the correct way was to use a paired input dataset as input (and Galaxy allows users to supply l ...
written 2.8 years ago by mrals8950
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Comment: C: Documentation for <collection> tag?
... Also, is there a simple method that I am unaware of to list available methods or keys, rather than hunting around for available methods or keys? ...
written 2.8 years ago by mrals8950
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Comment: C: Galaxy tool config for paired collection (list:paired) output?
... Related https://biostar.usegalaxy.org/p/13018/#13064 ...
written 2.8 years ago by mrals8950
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Comment: C: "Paired collection" as output
... Martin, now that this has been fully implemented, what is the recommended way of producing a list:paired collection as output? The tests have used nested collections as input but not as output https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/collection_nested_test.xml   Pleas ...
written 2.8 years ago by mrals8950

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Student 2.9 years ago, asked a question with at least 3 up-votes. For How do I retrieve filenames from a dataset collection inside tags?

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