These are chat archives for nextflow-io/nextflow

13th
Feb 2016
Evan Floden
@evanfloden
Feb 13 2016 20:13
I'm trying to run a Nextflow pipeline on a Mac using Docker and I'm getting the error '/bin/bash: .command.sh: No such file or directory'. However when I execute .command.sh from the work directory it runs fine.
Evan Floden
@evanfloden
Feb 13 2016 20:19
I've just found this issue post discussing the problem on GitHub: nextflow-io/nextflow#73. Will look into it
Paolo Di Tommaso
@pditommaso
Feb 13 2016 20:19
um, what if u run
Oops, yes make sure to have the work folder in a path under /Users/..
Evan Floden
@evanfloden
Feb 13 2016 20:21
Problem must be related to where I am running it from. I'm using an external drive as I have over 100 GB of RNA-Seq data and my Mac Book can't keep up!
Paolo Di Tommaso
@pditommaso
Feb 13 2016 20:23
Yes, don't forget that the Docker daemon on Mac run in a VM instance
By default the VM mount the /Users/ path on Mac
Evan Floden
@evanfloden
Feb 13 2016 20:24
Perfect, I keep in touch and let you know!
Paolo Di Tommaso
@pditommaso
Feb 13 2016 20:26
It should be possible to mount your device opening Virtual Box and setting the shared folder properly
Evan Floden
@evanfloden
Feb 13 2016 20:34
Great, seems to work fine now. Thanks a lot mate! ;)
Paolo Di Tommaso
@pditommaso
Feb 13 2016 20:35
:+1:
Have fun
Evan Floden
@evanfloden
Feb 13 2016 23:47
I can add the external drive to the shared folders on Virtual Box
And I can use docker-machine to ssh into the default machine and mount the Volumes dive
*drive
From inside the default machine I can see that the Volumes drive is mounted fine.
The problem appears to be that Nextflow is not adding this path /Volumes to when docker is executed.
Evan Floden
@evanfloden
Feb 13 2016 23:54
I modified the .command.run file by adding '-v /Volumes/ExternalDriveName:/Volumes/ExternalDriveName' to the docker run line.
This allows me to run the .command.run successfully in that it now finds the files on the external drive
However I have been unable to figure out how to get Nextflow to do this at run time.