James Gatter
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Recent activity by James Gatter
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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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Working fine for me! Thanks!
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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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I'm also getting this for a completely unrelated workflow. Docker went out yesterday and their website still seems somewhat unresponsive. That's just my suspicion anyway. Following this.
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