James Gatter
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Recent activity by James Gatter
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Hi Jason, The methods should be publicly viewable but I've shared the both tools with you just in case. Hope that helps! Oh and the dev snapshot that fails is 9, not 11! James
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Hi Jason, So for delocalization in the log, the wrong files are being delocalized. For example, read_string("metadata.txt") should have looked inside metadata.txt for the path to the desired file, ...
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Hey Jason, I ran it in alexandria/dropseq_cumulus/1. sco.scp.metadata.txt and other files are generated by Cumulus workflow, but they are wrapped in the Array[File] output_scp_files. In dropseq_cum...
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From yesterday and today, we've had 4 or 5 people in our lab encounter this problem when using cumulus/bcl2fastq and cumulus/dropseq_workflow. It seems that some tasks complete delocalization succe...
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Thanks Sushma!
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They seemed to have fixed it!!!https://github.com/DataBiosphere/terra-docker/blob/master/terra-jupyter-bioconductor/CHANGELOG.md
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With a new runtime it still didn't work! `Sys.getenv()` prints only the text below. I think maybe I'm using one of the old custom images (us.gcr.io/broad-dsp-gcr-public/terra-jupyter-bioconductor:0...
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bucket <- Sys.getenv('WORKSPACE_BUCKET')Returns an empty string for me. Hmm was the variable changed? Edit: print(Sys.getenv()) does not show any environmental variable that corresponds to it. 'CLU...
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Try fixing your docker parameter in the WDL: docker: "cumulusprod/cellranger:3.0.2"
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Huh, interesting. Also I can still pull the docker image locally. This seems to be something that we'll have to wait on.
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