Moderator: jmchilton

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jmchilton1.1k
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Posts by jmchilton

<prev • 78 results • page 1 of 8 • next >
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Answer: A: "Tool error: Unable to finish job" on the DOCKER version of galaxy, but not for
... Is the standard output and error for the datasets the same between the Docker and Planemo machine runs? It could be a difference with the version of Galaxy - if you are using a new (say 18.01) Docker container that is going to have different BAM handling than for instance a Galaxy running 17.09 whic ...
written 10 weeks ago by jmchilton1.1k
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Answer: A: How to write tests for tools that access built-in data from the data tables
... There is some documentation on how to do this here http://planemo.readthedocs.io/en/latest/writing_how_do_i.html#test-index-loc-data, I hope that helps. ...
written 3 months ago by jmchilton1.1k
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Answer: A: planemo test - mysterious samtools dependency
... That message I think it generated from the upload tool - it shouldn't break your tests as long as you aren't uploading bam files as inputs to the tool tests and can safely be ignored in most cases. The next version of Galaxy will no longer have a samtools dependency as part of the upload process at ...
written 7 months ago by jmchilton1.1k
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Answer: A: Download all history including data collection and nested data collections
... Unfortunately this is not possible yet, history export doesn't include collections. There is an open pull request from the community here (https://github.com/galaxyproject/galaxy/pull/4532) so we are getting closer. Hopefully this will be available in 18.01. Sorry. ...
written 9 months ago by jmchilton1.1k
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Answer: A: Batch workflow with two different inputs each time?
... I think you are essentially right about the concept of "paired" lists in Galaxy - they are meant to be of the same datatype. That said I think collections might still be the tool to use in general. Collections have the concept of order and identifiers for elements that are meant to allow this sort o ...
written 16 months ago by jmchilton1.1k
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Answer: A: Output dataset collection is empty
... I'd strongly encourage you to do this without the ``__new_file_path__`` stuff - that will be interpreted literally instead of being expanded in various places. You tool is given a clean working directory - I would just create files there - it works more cleanly and robustly with different deployment ...
written 18 months ago by jmchilton1.1k
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Answer: A: tool.xml : multiple but optional data
... I'm very sorry for the inconvenience and counter intuitiveness of the way empty selections are handled here. I've opened a PR against Galaxy to spell out what is going on in the documentation and to provide an example of how to work with an empty selection drawing from your example. It is here - htt ...
written 22 months ago by jmchilton1.1k
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Answer: A: get dataset datatype in tool
... I think what you are looking for is discussed in depth here - http://planemo.readthedocs.org/en/latest/writing_how_do_i.html#check-input-type-in-command-blocks. Hope this helps. ...
written 2.5 years ago by jmchilton1.1k
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Answer: A: Sending Files over Pulsar with a Local Tool
... There is not currently a way to do this. This is a serious deficiency in the way Pulsar operations. The work around is to make the script executable directly and place it on Pulsar's PATH manually - so the tool XML will not have an interpreter tag for instance. I hope that with the April release of ...
written 2.5 years ago by jmchilton1.1k
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Answer: A: galaxy setting problem on network
... You have configured Galaxy correctly it appears. Neither 0.0.0.0 or 127.0.0.1 are what you would use. You'll have to find the IP address of the machine (e.g. using the ifconfig command-line tool, your administration panel for your OS, or a service like http://whatismyipaddress.com/). If your IP addr ...
written 2.6 years ago by jmchilton1.1k

Latest awards to jmchilton

Scholar 12 weeks ago, created an answer that has been accepted. For A: Galaxy Upload Tool - Genome Version
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: How to write tests for tools that access built-in data from the data tables
Scholar 9 months ago, created an answer that has been accepted. For A: Galaxy Upload Tool - Genome Version
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Download all history including data collection and nested data collections
Guru 9 months ago, received more than 100 upvotes.
Scholar 16 months ago, created an answer that has been accepted. For A: Galaxy Upload Tool - Genome Version
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Batch workflow with two different inputs each time?
Scholar 22 months ago, created an answer that has been accepted. For A: Galaxy Upload Tool - Genome Version
Scholar 2.5 years ago, created an answer that has been accepted. For A: get dataset datatype in tool
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: local galaxy in Windows OS
Teacher 3.1 years ago, created an answer with at least 3 up-votes. For A: Bioblend - toolClient.run_tool does not work with more than one params ?
Scholar 3.4 years ago, created an answer that has been accepted. For A: Pulsar Error on Windows
Scholar 3.6 years ago, created an answer that has been accepted. For A: Accessing files created from the history
Scholar 3.6 years ago, created an answer that has been accepted. For A: Accessing files created from the history
Teacher 3.6 years ago, created an answer with at least 3 up-votes. For A: Upload directory paths
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Upload directory paths
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Upload directory paths
Teacher 3.8 years ago, created an answer with at least 3 up-votes. For A: Upload directory paths
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Upload directory paths
Scholar 3.9 years ago, created an answer that has been accepted. For A: Accessing files created from the history
Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: Tool XML Schema/DTD
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Upload directory paths

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