These are chat archives for nextflow-io/nextflow

23rd
Jul 2018
KochTobi
@KochTobi
Jul 23 2018 12:01

Hi there, how can I specify the ami that nextflow will use for spot requests? I tried

cloud {
  region = 'us-east-1'
  imageId = 'ami-803635ff' // this is my custom AMI 
  instanceType = 't2.micro'
}

But somehow all instances use amzn-ami-2017.09.l-amazon-ecs-optimized (ami-aff65ad2)

Paolo Di Tommaso
@pditommaso
Jul 23 2018 12:05
that's how it should be done
it was reported your AMI when you executed nextflow cloud create command ?
KochTobi
@KochTobi
Jul 23 2018 12:08
No I started it on my local machine. nextflow run tutorial.nf -w 's3://my-path' --verbose It did use other configurations like awscli that are defined in the same file.
Paolo Di Tommaso
@pditommaso
Jul 23 2018 12:09
not sure to understand, however before it asks for confirmation showing all current setting
make sure it matches your expected ones
KochTobi
@KochTobi
Jul 23 2018 12:13
When I use nextflow cloud create test It reports ERROR ~ Not a valid config attribute: 'region'
Paolo Di Tommaso
@pditommaso
Jul 23 2018 12:14
I think it's quite self-explicative
tbugfinder
@tbugfinder
Jul 23 2018 12:17
region is a parameter in aws config or use environment variable.
micans
@micans
Jul 23 2018 16:43
@pditommaso just saw your message about groupKey(). I can't try it before tomorrow, but it sounds great, with a nice syntax localised to tuple(). Very eager to try it! :+1: :+1: :+1:
Paolo Di Tommaso
@pditommaso
Jul 23 2018 16:45
No hurry (I'm going to the beach :))
Mike Smoot
@mes5k
Jul 23 2018 22:28
Hi @pditommaso if I want to add a mount point to the job container running in AWS batch, do I need to write my own job definition or is there another way? Just setting docker.runOptions or process.containerOptions doesn't seem to do the trick.