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GRIDSS: the Genomic Rearrangement IDentification Software Suite
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Docker gridss image cannot find reference genome #634

Closed mxiong2 closed 1 year ago

mxiong2 commented 1 year ago

The reference genome path is specify correctly, but I consistently get an error to set the reference location. Any thoughts?

Thu Jul 6 14:46:02 UTC 2023: Missing reference genome /media/sf_ncbi/GRCh38.d1.vd1.fa. Specify reference location using the --reference command line argument

"exit $EX_USAGE" command completed with exit code 64.

The underlying error message can be found in /media/sf_ncbi/gridss_out/gridss_tmp/gridss.full.20230706_144602.df195842c4e0.371.log

d-cameron commented 1 year ago

Have you mounted the reference genome directory in the docker image? Docker paths are relative to the image itself, not the host paths and the docker image only has access to the paths on the host file system that are explicitly mounted.

On Fri, 7 July 2023, 12:48 am mxiong2, @.***> wrote:

The reference genome path is specify correctly, but I consistently get an error to set the reference location. Any thoughts?

Thu Jul 6 14:46:02 UTC 2023: Missing reference genome /media/sf_ncbi/GRCh38.d1.vd1.fa. Specify reference location using the --reference command line argument

"exit $EX_USAGE" command completed with exit code 64.

The underlying error message can be found in /media/sf_ncbi/gridss_out/gridss_tmp/gridss.full.20230706_144602.df195842c4e0.371.log

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mxiong2 commented 1 year ago

Thanks d-cameron,

Do all path need to be mounted into the docker image? i.e the temp directory , output directory?

d-cameron commented 1 year ago

https://github.com/PapenfussLab/gridss/blob/master/docker/run_cohort_from_csv.sh#L117 is a good example of the recommended docker mounting points.

d-cameron commented 1 year ago

Temp directory does not (since /tmp exist in the image and you don't need anything out of it when you're done) but the input and output directories (including the working directory) should be mounted.