Fails to run local installation

[jorgedch]

Functionality

openjournals/joss-reviews#4517

• Installation:

1. Fails to run local installation command docker-compose build on Mac OS 12.4:

#0 110.6   Attempting uninstall: pyyaml
#0 110.6     Found existing installation: PyYAML 5.1.2
#0 110.6 Pip subprocess error:
#0 110.6 ERROR: Cannot uninstall 'PyYAML'. It is a distutils installed project and thus we cannot accurately determine which files belong to it which would lead to only a partial uninstall.
#0 110.6
#0 110.6
#0 110.6 failed
#0 110.6
#0 110.6 CondaEnvException: Pip failed
#0 110.6
------
failed to solve: executor failed running [/bin/sh -c conda env update -n base --file /salmon/salmon.yml --prune]: exit code: 1

[stsievert]

Hm... I can't reproduce.

Reproduction process

The command conda env create -f salmon.yml completed successfully for me with conda 4.10.3, the version specified in the Dockerfile.

Building the container also worked for me (with Docker Desktop on macOS 10.14). I ran these commands:

git clone https://github.com/stsievert/salmon.git
cd salmon
docker-compose build
docker-compose up -d --remove-orphans

I've deployed a fix in ced3cce in #139 (which is also the latest release). Do you want to try that commit and see if it works?

---

Perhaps a better question... why are you trying to build the Docker containers locally? I can let you run through the Amazon AWS install process at https://docs.stsievert.com/salmon/installation.html#experimentalist.

[jorgedch]

Yes, I run the commands that you mention (so it is already the latest release), but it was getting stuck in the docker-compose build step:

git clone https://github.com/stsievert/salmon.git
cd salmon
docker-compose build

I've been running this process as it is included in the installation docs, but you are right, this step is indicated as relevant for developers and not for experimentalists. That being said, after pulling your latest changes in the review-comments branch (#139) it installs and runs correctly, so from all sides we can close this issue :)