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Fix permissions for Singularity compatibility #34

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dleehr opened this issue Jan 31, 2018 · 0 comments
Open
1 task

Fix permissions for Singularity compatibility #34

dleehr opened this issue Jan 31, 2018 · 0 comments

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@dleehr
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dleehr commented Jan 31, 2018

Singularity can pull and run Docker images. However, since the command does not run as root, there are permission issues when trying to run some of the containers. This issue will track these bugs:

[dcl9@c1-05-2 ~]$ singularity exec docker://dukegcb/fastqc:0.11.4 fastqc
Docker image path: index.docker.io/dukegcb/fastqc:0.11.4
Cache folder set to /gpfs/fs0/home/dcl9/.singularity/docker
Creating container runtime...
/.singularity.d/actions/exec: 9: exec: fastqc: Permission denied
  • fastqc
johnbradley added a commit that referenced this issue Feb 1, 2018
@johnbradley
Fix chmod command to be singularity compatible
fb22ef4 
When using this docker image under singularity the fastqc
command didn't have permissions to run. #34
@johnbradley johnbradley mentioned this issue Feb 1, 2018
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@johnbradley johnbradley mentioned this issue Feb 12, 2018
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@dleehr