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Sign up12 June 2019, Charlottesville: Bioinformatics in a High-Performance Computing Environment #573
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Daniel-Mietchen
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Jun 12, 2019
Daniel-Mietchen
added this to the 2019-06 milestone
Jun 12, 2019
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Good mix of people in the room, including some people from iGEM Virginia with whom I was trying to get in touch anyway, following the synthetic biology symposium last week (cf. #568 ). In the afternoon, there will be room to discuss what software is/ should be running on the UVA HPC cluster Rivanna (see my separate notes on that). I'd like to use a MyBinder/ Docker/ Wikibase combo, and I'd like to learn more about the different file formats used in sequence analysis as well as about dark taxa. |
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Another thing that's on my mind in this context is how things like http://wikigenomes.org/ can be integrated into sequence analysis workflows, or https://wikidp.org/ into software curation workflows. |
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I asked about how the environmental footprint of Rivanna is managed, and the VP for IT was mentioned as overseeing that. Will contact them. |
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as allocation, users can use "rivanna-training" up to certain limits. |
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For large file transfers, use Globus. |
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For the hands-on, I am using the Terminal under rivanna-portal, along with instructions from |
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The |
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after launching the ijob, |
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to get a list of all of a user's Rivanna jobs on that host machine, type |
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to get a list of most recently run jobs, type |
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If there is no scratch directory, then instead of |
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met Sarah French. will send email to follow up. under |
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Both the iGEM team and Sara are working on styrofoam. |
Daniel-Mietchen commentedJun 12, 2019
as per
https://education.cadre.virginia.edu/#/workshop/1596
and
https://workshops.somrc.virginia.edu/lesson/hpc-bioinformatics/