Closed Mnikley closed 6 months ago
Hi @Mnikley,
thanks for the report, and apologies for the lack of transparency. The simple-docker
requires a valid API key in the environment and in general is an older experimental branch. The main
branch is the one that should work. I added some info in the README of the simple-docker
branch to clarify this.
As for the main
branch, for me this works fine with
git clone https://github.com/biocypher/meta-graph.git
cd meta-graph
docker compose up -d
Can you make sure to remove all remaining Docker components from previous runs (the volumes can be a problem if they are not removed properly), using docker compose down --volumes
?
Hey @slobentanzer,
thank you for your reply. Using the main
branch helped me to progress, thank you. Eventually I could start the stack after fixing the line endings of the bash scripts scripts/build.sh
and scripts/import.sh
, which were causing an issue due to cloning the repository on Windows with autocrlf
enabled (git config --get core.autocrlf
-> true
):
docker-compose down
git checkout main
docker-compose up -d
time="2024-04-16T09:16:24+02:00" level=warning msg="The \"BIOCYPHER_GITHUB_PROJECT_TOKEN\" variable is not set. Defaulting to a blank string."
[+] Building 0.0s (0/0) docker:default
[+] Running 5/5
✔ Network meta-graph_default Created 0.0s
✔ Volume "meta-graph_biocypher-meta-graph_data" Created 0.0s
✘ Container build service "build" didn't complete successfully: exit 1 0.0s
✔ Container import Created 0.0s
✔ Container deploy Created 0.0s
service "build" didn't complete successfully: exit 1
docker-compose logs
time="2024-04-16T09:16:29+02:00" level=warning msg="The \"BIOCYPHER_GITHUB_PROJECT_TOKEN\" variable is not set. Defaulting to a blank string."
build | /src/scripts/build.sh: line 2: cd: $'/usr/app/\r': No such file or directory
build | cp: target '.'$'\r' is not a directory
build | cp: cannot stat 'config/biocypher_docker_config.yaml': No such file or directory
build |
" does not exist.and "install
build |
build | Did you mean this?
build | install
build | python3: can't open file '/app/create_knowledge_graph.py\r': [Errno 2] No such file or directory
build | chmod: cannot access 'biocypher-log': No such file or directory
dos2unix
dos2unix scripts/build.sh
dos2unix scripts/import.sh
Also I was wondering if you deliberately use your image v1.0.0 in the docker-compose file, as I saw that you already released versions 1.1.0 and 1.1.1 ?
Thanks again, Matthias
Hi Matthias, thanks for the explanation, I unfortunately do not work on Windows, and these path things are somewhat of a mystery to me. :)
Do you think this should be explained somewhere, or should we even take some measures to prevent this from happening for other Windows users? @nilskre FYI
Building the docker-compose.yml from both, the master as well as the simple-docker branch, fails.
Background information
Steps to reproduce