Former User of DNAx Community_55
Posts
Recent activity by Former User of DNAx Community_55
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How can we set a retry policy on dx run jobs?
This document in the handbook for the UK Biobank RAP states, "If you decide not to use a retry policy, occasionally, some jobs may fail due to sample-specific issues or due to external factors suc...
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How can we execute modified applets without creating duplicated data?
From what I can tell from experiments, there is no way to tell applets to overwrite output files or to respect the output from previous applet versions. While this isn't a problem thanks to caching...
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Why do our forum passwords need to be reset every 3 months?
(At least, this is inference since I last set my password 3 months ago and upon logging in, I was asked to reset it again.)
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I'm trying to use "dx upload filename --destination "project/path" from my university network but I'm getting errors like: urllib3.exceptions.ProtocolError: ('Connection aborted.', TimeoutError('The write operation timed out')) Is there an outage?
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How to use more than 100 machines simultaneously
Cloud computing has many downsides, but one of its upsides is (usually) simultaneous access to large numbers of machines on demand. However, with DNANexus, I have not been able to access more than ...
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How to overwrite preexisting file with the same name and path when using dx upload?
Let's say I have a file at /tmp/file.txt. Normally, if I copy another file to /tmp/file.txt, the file.txt contents are just updated with whatever I put there. However, it seems that when I run `dx ...
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dxfuse mounted filesystem eventually fails with "transport endpoint is not connected"
I was opening a bgi file directly from the dxfuse mounted filesystem with a JupyterLab instance. I soon started getting "transport endpoint is not connected" errors. After that, nothing would load ...
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Specify a normal filename / filepath for input JSON using WDL
From what I can tell so far from experimentation, it is possible to hardcode file paths within a WDL on DNANexus, but it is not possible to provide a path in the input.json file. For example, in t...
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Extraneous jobs for input and output when running WDL workflows?
When I run WDL workflows that have input{} and output{} blocks in addition to my command{} block, the Monitor tab shows that there are 3 jobs: "common", the actual task, and then "outputs" (screens...
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dxfuse: automatically mount /mnt/project on custom Docker images?
My question is whether it's possible for dxfuse to automatically mount the project's folder with dxfuse under /mnt/project when using our own custom Docker images.
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