Moderator: jmchilton

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jmchilton1000
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Posts by jmchilton

<prev • 74 results • page 1 of 8 • next >
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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 10 weeks ago by jmchilton1000
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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 4 months ago by jmchilton1000
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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 8 months ago by jmchilton1000
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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 16 months ago by jmchilton1000
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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 16 months ago by jmchilton1000
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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 17 months ago by jmchilton1000
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Answer: A: [Tool Config] How to enforce cleanup tasks (shell commands) on job cancelation
... There is no such configuration point in Galaxy, you may wish consider creating an issue for this https://github.com/galaxyproject/galaxy/issues if you consider it important - but it seems very niche and I am not sure it would a project priority so working through it an opening a pull request would p ...
written 17 months ago by jmchilton1000
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Answer: A: Passing job_resource_params_conf options to queue
... You must define a dynamic job destination (https://wiki.galaxyproject.org/Admin/Config/Jobs#Dynamic_Destination_Mapping) to consume these paramters  and produce a job destination that maps the parameters to the queue parameter you are wish to use. If your job destination function has a parameter na ...
written 17 months ago by jmchilton1000
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Answer: A: planemo test failure (virtualenv problem?)
... I've made a number of changes to planemo to continue to try to address recent changes in Galaxy (requiring a virtualenv, using wheels instead of eggs, etc...) I suspect just updating planemo will correct these errors, can you verify? ...
written 17 months ago by jmchilton1000
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Answer: A: Pulsar gives "[Errno 2] No such file or directory:" for data managers and UCSC G
... Youri - I don't think you are doing anything wrong here. Pulsar overrides the job building in a lot of ways - but there are many cracks where Galaxy plumbing allows things to get through. My guess here is that these outputs are being defined in galaxy.json and Pulsar isn't parsing that file to find ...
written 17 months ago by jmchilton1000

Latest awards to jmchilton

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Batch workflow with two different inputs each time?
Scholar 8 months ago, created an answer that has been accepted. For A: Galaxy Upload Tool - Genome Version
Scholar 16 months ago, created an answer that has been accepted. For A: get dataset datatype in tool
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: local galaxy in Windows OS
Teacher 24 months 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 2.2 years ago, created an answer that has been accepted. For A: Pulsar Error on Windows
Scholar 2.4 years ago, created an answer that has been accepted. For A: Accessing files created from the history
Scholar 2.4 years ago, created an answer that has been accepted. For A: Accessing files created from the history
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Upload directory paths
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Upload directory paths
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Upload directory paths
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Upload directory paths
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Upload directory paths
Scholar 2.8 years ago, created an answer that has been accepted. For A: Accessing files created from the history
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Tool XML Schema/DTD
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: Upload directory paths

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