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Docker image missing svtyper #213

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mcv053 opened this issue Jan 22, 2023 · 0 comments
Open

Docker image missing svtyper #213

mcv053 opened this issue Jan 22, 2023 · 0 comments

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@mcv053
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mcv053 commented Jan 22, 2023

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?

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