This is a docker image with a few helpful features (R, tidyverse, stan, bioconductor) for statistical and ML work, I use it on dnanexus machines.
Usage:
dx run my_cwic --ssh -i "image=nicokist/dnanexus_working_environment"
If you want to use the highly experimental read/write mode:
dx run my_cwic --ssh -i "image=nicokist/dnanexus_working_environment" -iproject_mount_options='-w'
If you want a particular Azure instance type:
dx run my_cwic --ssh -i "image=nicokist/dnanexus_working_environment" --instance-type azure:mem1_ssd1_x8
You'll find your project directory mounted as a filesystem on /project/. Note that there are some large conceptual differences between dnanexus storage blobs (more similar to Amazon S3 and google cloud storage) and filesystems, which are resolved by dxfuse. The biggest thing you can do to limit these annoyances is to avoid having multiple files with the same name stored in DNANexus.
If a file does not show up immediately on either the filesystem or platform.dnanexus.com, you may want to run dxfuse-sync.
Note that it may take some time (~5 min) to download the docker image from docker.com, during this time the message "Waiting for the cwic container to start.." will be shown.
You may want to run dx login to ensure you have the correct credentials within the cwic environment.
By default these containers are not persistent.
dx-toolkit needs to be installed.
The my_cwic applet needs to be present in the project you're working on. Either copy it over from another project or build it as follows:
git clone https://github.com/dnanexus/cwic.git
cd cwic
dx build -f -d my_cwic
(in my testing this didn't work so well when using the read/write mode, but it worked well enough when only reading.)
dx login
mkdir /mnt/project2
dxfuse-mount /mnt/project2/ DNANEXUS_PROJECT_NAME
ls /mnt/project2