Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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For this and similar problems, I usually prefer using "dx find data --name "*.xyz" --brief" to get properly formatted file ids and later use this list of ids in a custom bash one-liner/script (json...
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There is a couple of options how to manage software dependencies in the custom applets. I remember that in the past I used for example: a) "execDepends" section in the dxapp.json (https://documenta...
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https://discuss.hail.is/t/exporting-data-from-matrixtable-into-tsv/2406
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I think that saving it to csv and manipulating the data on hdfs might resolve this:https://community.dnanexus.com/s/question/0D5t0000045I12HCAS/where-does-saved-data-go-on-a-jupyter-spark-cluster
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Just for more information, I am sharing here my experience with building DNAnexus workflow manually. I am not sure if this is a good fit for you use case and if this could be combined with Swiss Ar...
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Another thing (not tested on my side) might be using tools such as dxda for download (https://github.com/dnanexus/dxda).
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Not knowing much about this, but I would first consult Rate card (maybe you did). There is a list of all available instance types with mapping to EC2 Instance Type (AWS). If you select a specific i...
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Do you want to access that file via dxfuse, i.e. /mnt/project/...? If so please refer here: https://community.dnanexus.com/s/question/0D5t000003vAWYxCAO/it-seems-that-the-recently-dx-uploaded-files...
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Hi! Command in the following format worked for me and this extracted just one chromosome from CRAM without downloading the entire CRAM and reference genome: samtools view -b -T /mnt/project/ref_gen...
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It looks like the github page https://github.com/weizhou0/GATE#uk-biobank-gwas-results is in progress, as the uk-biobank-gwas-results section is missing and it is not clickable. It might be worth t...
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