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simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
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Cannot run docker image for VirSorter (docker: Error response from daemon: Mounts denied:) #16

Closed jolespin closed 6 years ago

jolespin commented 6 years ago

Are there any step-by-step directions to get this up and running? I've never used a docker before. I can also install each of those packages and set up symbolic links if necessary. I have the data ready to go but can't figure out how to run VirSorter.

Directories:

virsorter-data

/Applications/VirSorter/virsorter-data/ image

Input Fasta

/Users/jespinoz/Viral/iter5__bin_34.fa

jespinozlt-osx:Viral jespinoz$ docker pull discoenv/virsorter:v1.0.3
v1.0.3: Pulling from discoenv/virsorter
7ccc78f8af6d: Already exists
a3ed95caeb02: Already exists
fc159b297d00: Already exists
ab2379c3299b: Already exists
2f74b287b011: Already exists
198339110edc: Already exists
8e438e92597e: Already exists
805903dd3399: Already exists
4e650a49b37b: Already exists
8d688621ce05: Already exists
e1f20323421e: Already exists
45535f86a2c5: Already exists
37797ac35b59: Already exists
37b655e6666e: Already exists
357d5747771f: Already exists
b030a34166a7: Already exists
Digest: sha256:02c0acb6176ecc3f0faa984d3506c529323e0c1e5a62a90b63f826dcf97b5101
Status: Image is up to date for discoenv/virsorter:v1.0.3
jespinozlt-osx:Viral jespinoz$ docker run -v /Applications/VirSorter/virsorter-data:/data -v /Users/jespinoz/Viral/:/wdir -w /wdir --rm discoenv/virsorter:v1.0.3 --db 2 --fna /wdir/iter5__bin_34.fa
docker: Error response from daemon: Mounts denied:
The path /Applications/VirSorter/virsorter-data
is not shared from OS X and is not known to Docker.
You can configure shared paths from Docker -> Preferences... -> File Sharing.
See https://docs.docker.com/docker-for-mac/osxfs/#namespaces for more info.
.
ERRO[0000] error waiting for container: context canceled
simroux commented 6 years ago

We don't have any VirSorter-specific step-by-step instruction for running the docker container, although if you did not use docker before, you may want to try the simpler examples in the docker tutorial (https://docs.docker.com/docker-for-mac/) to make sure everything works before running VirSorter.

Alternatively, VirSorter is also available on CyVerse, where you simply have to upload your data (in a private space) and then click a button to run the tool.