TRF path error while running a Docker about tetools HOT 5 CLOSED

You can specify a path to TRF manually if it's not in your PATH. I expect that this should work for you:

./dfam-tetools.sh --trf-path=./TRF.linux64

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Ran into a similar problem. I did specify the TRF path but still getting the same error even though it is executable

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I made a mistake earlier when I referred to --trf-path=. It is --trf_prgm=.

@jageis-fldm I think the issue there is that getopt is very different on macOS, so I will need to work around that somehow. In the meantime, you can run it manually. This command would start the container the same way that dfam-tetools.sh would have; note that you do need to use the Linux version of TRF:

docker run -it --rm --mount type=bind,source="$(pwd)",target=/work --mount type=bind,source="./trf409.linux64",target=/opt/trf,ro --user "$(id -u):$(id -g)" --workdir "/work" --env "HOME=/work" "dfam/tetools:1"

However, I am not sure if it will work as expected on Mac and I do not have Docker for Mac set up to test it with.

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Thanks for the prompt response! Appears to be working now...

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I have updated dfam-tetools.sh in commit ac133a2 to only use commands that are available on macOS, so I believe the script should work now although I have still not tested the actual container.

You can re-run curl -sSLO https://github.com/Dfam-consortium/TETools/raw/master/dfam-tetools.sh to get the latest version.

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