But what I need to do is pass to all but one -- so I need tool-specific exclusions.
use case: on rivanna, you have to mount /ext in order to use nameservers, like -B /ext:/ext with singularity. otherwise, for example, prefetch doesn't work. So, I put /ext into the global mounts in my bulker config. BUT... this breaks the bioconductor R image, for some reason, which cannot have the host /ext mounted. So, I'd like to make /ext always mounted, except for the R image.
right now I just load it for all, but after every bulker load I have to manually delete that line from R containerized executable script, which is a pain.
Right now you can list variables and mount points to pass to all containers.
You can also use tool-specific args to pass a variable or mount point to a single container. (https://github.com/databio/bulker/issues/7)
But what I need to do is pass to all but one -- so I need tool-specific exclusions.
use case: on rivanna, you have to mount
/extin order to use nameservers, like-B /ext:/extwith singularity. otherwise, for example, prefetch doesn't work. So, I put/extinto the global mounts in my bulker config. BUT... this breaks the bioconductor R image, for some reason, which cannot have the host/extmounted. So, I'd like to make/extalways mounted, except for the R image.right now I just load it for all, but after every
bulker loadI have to manually delete that line from R containerized executable script, which is a pain.