aligning on file paths

[EdGreen21]

looks like there's a misalignment between teams regarding the runner:

1. WORKDIR being set to /apps, @KyleTCL using /scripts
2. ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "predictcr", "predicTCR_runner"] @KyleTCL using script.sh
3. DKFZ specific proxy settings now appear resolved on our side by editing /etc/docker/daemon.json rather than passing these env variables in the docker run command

[lkeegan]

looks like there's a misalignment between teams regarding the runner:

1. WORKDIR being set to /apps, @KyleTCL using /scripts
2. ENTRYPOINT ["conda", "run", "--no-capture-output", "-n", "predictcr", "predicTCR_runner"] @KyleTCL using script.sh

The WORKDIR and ENTRYPOINT of the docker image should not need to be modified, instead the PREDICTCR_RUNNER_SCRIPT_DIR environment variable should be set to point to the scripts folder, as described here: https://github.com/ssciwr/predicTCR/tree/main/runner#use

@KyleTCL let me know if this isn't working for you

4. DKFZ specific proxy settings now appear resolved on our side by editing /etc/docker/daemon.json rather than passing these env variables in the docker run command

great!