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Updates to documentation for initial setup #13

Merged
merged 10 commits into from
Jan 10, 2019
Merged

Updates to documentation for initial setup #13

merged 10 commits into from
Jan 10, 2019

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ghost
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@ghost ghost commented Apr 16, 2018

Adds documentation to bypass setup errors.

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Please also write down the documentation for how to install docker-machine and add to your path variable- this is the starting page https://docs.docker.com/machine/install-machine/#install-machine-directly but it assumes you have sudo ; in our case we want to just install it "personally".

cp samples/*.fastq.gz treeshop/primary/original/TEST/

Spin up a single cluster machine:
Spin up a single cluster machine (make sure you have created your SSH key):
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Provide instructions for:
a) checking if you already have an "~/.ssh/id_rsa" private+public keypair files that don't require a password
b) if you don't have a keypair, how to create it

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Another thing to incorporate at the end:

  • how to spin down machines when done
  • the info from Rob's April 12 email "Floating IPs" about how to clear the IP addresses after spinning down machines.

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e-t-k commented May 7, 2018

Thank you @aglyle ; I'm satisfied.

@klearned , passing this to you -- could you please do a readthrough of the new treeshop.md for potential improvements?

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klearned commented May 8, 2018

Yes, I'll read through the new treeshop.md today

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ghost commented May 31, 2018

Thanks for the comments @klearned!
@e-t-k can you take a final look at these changes and I'll ping Rob to merge the branch.

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e-t-k commented May 31, 2018

@aglyle looks great. I approve this doc.

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ghost commented May 31, 2018

@rcurrie Updates to the treeshop.md ready to be merged with master. Let me know if there's anything you want me to change.

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rcurrie commented Jun 1, 2018 via email

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Some specific comments below, but in general suggest this should be very prescriptive step by step so that someone can bring up a single group of machines, process, and shut down all with the HEAD of master.

treeshop.md Outdated

#echo mypath=$PATH
export PATH=$HOME/bin:$PATH
export PATH=$PATH:/pod/pstore/groups/treehouse/sratoolkit/sratoolkit.2.8.2-1-centos_linux64/bin/:/scratch/<username>
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Shouldn't need SRA

treeshop.md Outdated

fab down

#### Select machines
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Suggest we remove all of this. Most people should follow a very rote path: up process down, repeat. At the very end have a section called 'advanced' where you point them to the fabric and docker-machine docs and allude to this but not spell it out. Having subsets of machines running, and the need to reset, is asking for problems for those that don't know how all this really works.

treeshop.md Outdated
@@ -155,3 +275,7 @@ quite a bit of extra provenance by writing methods.json files as well as organiz
per the Treehouse storage layout. That said if you have some custom additional pipelines you want to
run its fairly easy to just add another target to the Makefile and then copy/paste inside of the
fabfile.py process method.

If using multiple versions of the fabfile, you can select which version to use via the -f flag:
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Also remove this toward a very prescriptive approach to these docs. The advanced pointer can list capabilities (running multiple fab files, multiple clusters via fab and docker-machine) but not spell it out. Multiple fab files plus multiple clusters to someone not familar with distributed computing. Also if they have an editied fabfile the hash in the methods.json will not be correct and we'll have no way to sort out what happened after the fact.

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ghost commented Jun 5, 2018

@rcurrie Incorporated your comments. Removed sections that we expect users to know (SSH Key creation), unsure if you wanted to keep PATH setup or not, but it's removed in the latest version. Also moved documentation for shutting down select machines and different fabfiles to links in the options. Removed shutting down IPs as it is Treehouse specific.

@e-t-k e-t-k merged commit 9e028eb into master Jan 10, 2019
@e-t-k e-t-k deleted the 12_aglyle branch January 10, 2019 22:30
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4 participants