While docker is probably the older and well established container technology, there are use cases where some Docker concepts are show-stoppers or difficult to work around.
msconvert will very often be used to convert MS raw data
on a network file share such as NFS. Because docker containers
are executed through the dockerd daemon which is by default running
as root user, the container can not write the converted files
back to the NFS share (unless you do some uid remapping magic,
or run NFS as no_root_squash).
We don't (yet ?) have a recipe to create a Singularity pwiz container image, but here are the steps to convert the Docker image to a Singularity image. This requires that the docker image can be pulled from a registry. You can run an insecure ad-hoc created local registry running in a container itself:
docker run -d -p 5000:5000 --restart=always --name registry registry:2
First, build the docker image as described in the README.md, and push it into a docker registry:
docker build --tag="phnmnl/pwiz-i-agree-to-the-vendor-licenses:latest" .
docker tag phnmnl/pwiz-i-agree-to-the-vendor-licenses localhost:5000/pwiz-i-agree-to-the-vendor-licenses
docker push localhost:5000/pwiz-i-agree-to-the-vendor-licenses:latest
As root you can then convert the docker image with instructions in Singularity
into a .simg image. The docker registry information, image name and tag
are in that Singularity recipe. We need --writable because we need to
write to the WINEPREFIX inside the container:
SINGULARITY_NOHTTPS=1 singularity build --writable pwiz-i-agree-to-the-vendor-licenses.simg Singularity
Now you are ready to execute the pwiz-i-agree-to-the-vendor-licenses.simg
as a normal user. We need to specify a temporary diectory
with -S /mywineprefix/, and we can optionally mount an NFS share that exists
on the host system with -B /nfs.
singularity exec -B /nfs -S /mywineprefix/ ./pwiz-i-agree-to-the-vendor-licenses.simg mywine msconvert /nfs/.../neg_MM8_1-A,2_01_9980.d -o $HOME/mzML`