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I found two mistakes in README for the usage of clinsv1.0 part:
docker image mrbradley2/clinsv:v1.0.1 does not exist in DockerHub, we can choose to pull v1.0;
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 $PWD/clinsv:/app/ref-data, or alternatively, change to -ref /app/ref-data/. In addition, at least in v1.0, the final -w argument is not existed, we need to delete it.
Hope you can fix these small bugs in README if I am correct, because it really bothers me several days, hope others can use this excellent tool smoothly.
The text was updated successfully, but these errors were encountered:
I found two mistakes in README for the usage of clinsv1.0 part:
refdata_path=$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.
The text was updated successfully, but these errors were encountered: