Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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It seems to me you should first download the file "output.vcf" to the cloud worker. As far as I can see from your screenshot, the file is located on DNAnexus project. You have basically two options...
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Hello {@005t000000BBrFkAAL}?, I looked into this and prepared some steps for you. You will need to run JupyterLab with Python/R. As a testing example vcf file, I used a publicly available snpeff an...
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Are you using Spark based JupyterLab?
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In order to convert and visualize UKB OCT data, it should not be tricky to install OCT Converter tool (https://github.com/marksgraham/OCT-Converter) in JupyterLab environment, do necessary OCT file...
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Dask looks great, will definitely read more about it.
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As I said, I think the "set -euxo pipefail" should do the trick. I might be wrong, but I would give it a chance.
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I had success installing devtools package once I installed all the missing system dependencies via JupyterLab Terminal: apt updateapt upgradeapt install libcurl4-openssl-devapt-get install libbz2-d...
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From the implementation snippet, it seems like the bash applet you run is yours and you have all control over it. If that is the case, you can try to add "set -euxo pipefail" on top of your main sc...
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You may want CLI approach rather and use "dx watch job-XXXX" that might have more information included in the log. In GUI, also make sure you show stdout as well as stderr.
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Did you use correct "download" command to get the above mentioned "ukbXXXXXX.csv" file? You may want to get the ICD10 data from RAP. For such data/field extraction, I normally use JupyterLab and e...
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