Stephen Fleming
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Activity overview
Latest activity by Stephen Fleming-
Stephen Fleming commented,
Thanks for this post! It was confusing to me that when I would "recreate" my runtime using a docker image, I would find that the same package installation problems had followed me to the new runti...
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Stephen Fleming commented,
Hi Jason, Okay, the example WDL you sent is very helpful. I wasn't sure if any computation could be done in the workflow block, but the example shows that WDL standard library commands can be exec...
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Stephen Fleming created a post,
Scatter: over chunks rather than for each
Hello! I have a specific question about scattering in a WDL. What I want to do is a lot like this scatter (file in file_array) { call task{input: file=file}} except that, in my case, it is horrib...
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Stephen Fleming commented,
Thanks Jason! With a suggestion from Luca D'Alessio, I have attempted this, which seems to work: BUCKET=$(cat gcs_delocalization.sh | grep -o '"gs:\/\/.*/call' | sed 's/\/call/"/' | head -n 1) ...
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Stephen Fleming created a post,
Cromwell execution directory
Cromwell question: is there an environment variable that I can access from within a running task's command block that specifies the Cromwell execution directory (google bucket) ?
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Stephen Fleming commented,
Okay thanks!
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Stephen Fleming commented,
runtime { ... monitor_image: quay.io/broadinstitute/cromwell-monitor} I believe you can do the above in a WDL, but then I am not clear on how to get the results. Denis Loginov any tips on ho...
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Stephen Fleming commented,
I don't know the best answer, but just wanted to throw a couple links up here for the next time I search for this: https://github.com/broadinstitute/dsp-scripts/blob/master/cromwell/methods/cromwel...
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Stephen Fleming commented,
Hi Jason, Yeah, I was a bit vague there. I was mainly referring to the fact that we have several workflows internally that all require particular versions of particular tools. As some of the tool...
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Stephen Fleming created a post,
Possible to clone a notebook VM?
Hello! I want to enable somebody else on my billing project to work in the exact same notebook environment I am working in. I realize that the real goal is to have a nice docker image so that you c...