I ran this in the latest docker image and got the following error:
panic: exec: "svtyper": executable file not found in $PATH
When I reload the docker image, and run smoove without arguments, it confirms that svtyper is indeed missing from the path:
Using default tag: latest
latest: Pulling from brentp/smoove
Digest: sha256:d0d6977dcd636e8ed048ae21199674f625108be26d0d0acd39db4446a0bbdced
Status: Image is up to date for brentp/smoove:latest
docker.io/brentp/smoove:latest
mcv053$ smoove
smoove version: 0.2.6
smoove calls several programs. Those with 'Y' are found on your $PATH. Only those with '*' are required.
*[Y] bgzip [ sort -> (compress) -> index ]
*[Y] gsort [(sort) -> compress -> index ]
*[Y] tabix [ sort -> compress -> (index)]
*[Y] lumpy
*[Y] lumpy_filter
*[Y] samtools
*[ ] svtyper
*[Y] mosdepth [extra filtering of split and discordant files for better scaling]
[Y] duphold [(optional) annotate calls with depth changes]
[ ] svtools [only needed for large cohorts].
...
Looking through the docker file, it seems like svtyper should be available. Is this a problem anyone else has encountered?
I ran this in the latest docker image and got the following error:
panic: exec: "svtyper": executable file not found in $PATHWhen I reload the docker image, and run smoove without arguments, it confirms that svtyper is indeed missing from the path:
Looking through the docker file, it seems like svtyper should be available. Is this a problem anyone else has encountered?