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KCCG / ClinSV

Robust detection of clinically relevant structural and copy number variation from whole genome sequencing data
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Small issues in README: wrong instructions for running clinsv1.0 #58

Open sunjh22 opened 7 months ago

sunjh22 commented 7 months ago

I found two mistakes in README for the usage of clinsv1.0 part:

  1. docker image mrbradley2/clinsv:v1.0.1 does not exist in DockerHub, we can choose to pull v1.0;
  2. the following volume mounting is wrong: refdata_path=$PWD/clinsv/refdata-b38 input_path=$PWD project_folder=$PWD/test_run docker run -v $refdata_path:/app/ref-data -v $project_folder:/app/project_folder -v $input_path:/app/input --entrypoint "perl" mrbradley2/clinsv:v1.0.1 /app/clinsv/bin/clinsv -r all -p /app/project_folder/ -i "/app/input/*.bam" -ref /app/ref-data/refdata-b38 -w because in this case, the reference directory will be $PWD/clinsv/refdata-b38/refdata-b38/, which will lead errors for cannot finding reference files. We can fix the mount point to -v $PWD/clinsv:/app/ref-data, or alternatively, change to -ref /app/ref-data/. In addition, at least in v1.0, the final -w argument is not existed, we need to delete it.

Hope you can fix these small bugs in README if I am correct, because it really bothers me several days, hope others can use this excellent tool smoothly.

J-Bradlee commented 2 months ago

Thank you for this @sunjh22 . I am working on cleaning a few things up on here and will fix all these bugs in a final release version of 1.1.