No cloudman

[Kenneth Daily]

Is it possible to use one of the flavors but disable cloudman? I'd just like to use CloudBioLinux to install all NGS-related software; I couldn't figure out where the cloudman stuff comes in and is configured.

Thanks!

[Brad Chapman]

Kenneth;
Absolustely, the 'ngs_pipeline_minimal' flavor is the one you'd want to
use for this. Practially, bcbio uses this for installation of third
party tools, so it's well tested and regularly used. You can use the
bcbio installer to get an isolated installation of tools into a
particular directory using CloudBioLinux under the covers:

https://bcbio-nextgen.readthedocs.org/en/latest/contents/installation.html#automated

Hope this helps,
Brad

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[Kenneth Daily]

Thanks Brad! I think I was shooting myself in the foot, as I was using 'ngs_pipeline_minimal'. However, I pre-cloudbiolinux install, I was running:

yum install -y cloud-init

I must have taken this from an example script I found on the interwebs; guess I thought it was a prerequisite. When I do this, within an Amazon VPC with which I am setting up my cluster, on boot it seems to try to access an external resource (169.254.169.254), which is rejected by the VPC, and the machine stalls when booting.