Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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Hello @Kathleen Keough?, that is great! I am really interested in your PheWAS research project. Could you please tell me more about on which type of data you apply the PheWAS R package?
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As another alternative for developing a WDL workflow - if cannot run docker on your machine - you can run a UKB RAP cloud worker app, such ttyd or cloud workstation and compile your WDL workflow th...
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As a non-batch testing job, are you able to get one of your Swiss Army Knife jobs Done? I mean just one vcf and its tbi in non-batch mode?
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In your dx generate_batch_inputs, I noticed the digit "2" in -iin2. I think this is incorrect syntax. In my understanding, SAK takes multiple inputs defined as "-iin", regardless of position of the...
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@Ben Busby?, please do you have any idea on which tool would be a good fit for this?
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In the JupyterLab, default "working" directory is /opt/notebooks/, so I think you can find your downloaded data there. An unrelated note, I am seeing that SUBJECTS_DIR is also a predefined variable...
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No need to use Nipype in order get Freesurfer commands. You can access Freesurfer from the JupyterLab Terminal: If you would like to know more about Docker on RAP:https://community.dnanexus.com/s/...
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Freesurfer, FSL and Nipype are part of the JupyterLab IMAGE_PROCESSING flavor. You can just launch Jupyter or work with Docker and do all your planned work on RAP. There are some training materials...
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There is also a possibility to call directly "dx describe", instead of "dx api ... describe". "dx describe" will not return a JSON object. If you would like to get a JSON object, you will need to a...
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Hello @Gary Burnett?, please would you be able to help with this Mutectcaller-related question?
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