I’ve been trying for several days to install a local instance of galaxy on a VM running Ubuntu 22.04. I’ve created a local, non-root galaxy user and started a conda virtual environment running python 3.7.6 (although I’ve also tried this with many other versions of python as well). The installation seems to go well until it stalls with the following message:
I have run the suggested command several times, and I’m told that caniuseis up to date. I have also tried a host of npx and npm commands to make updates as well. Even so, I keep hitting this wall.
After the message, the build essentially stalls until it eventually throws an error 134, and some message about javascript heap out of memory.
Has anyone run into this issue and found a work around?
Thanks for any help!
(P.S. thanks to @jennaj and @cjkeist for help at a previous installation question, see here)
The caniuse warning message is a red herring, the issue is most likely the OOM crash. The Galaxy client build requires a substantial amount of memory sadly and if you have a tiny VM it might be crashing it. How much RAM does the VM have? Try cleaning the VM’s RAM, activating Galaxy’s venv and run make client-production in the Galaxy root folder independently of Galaxy’s startup. Alternatively give the VM more RAM for the build after each Galaxy update (that’s the only time the client needs building).
I gave the VM 10 GB of RAM, which I hoped would be enough. I’ll try increasing the RAM as well as your other suggestion above. Thanks so much for the help! I’ll let you know if this fixes it.
I just tried running: make client-production. I’m getting a new error:
error citation-js@0.6.8: The engine "node" is incompatible with this module. Expected version ">=14". Got "12.22.9"
error Found incompatible module
info Visit https://yarnpkg.com/en/docs/cli/install for documentation about this command
make: *** [Makefile:177: client-node-deps] Error 1
I’m a bit lost, but I think the problem is with yarn (I get the same error running yarn in the console) and nodejs? Is it related to this post?
Regarding your second issue, that node version is quite old, and, indeed, incompatible. Galaxy, depending on the version you are using, should be installing and trying to use v16 or v18. What galaxy version are you trying to use?
Update: Making the changes to the Makefile you suggested, the sh run.sh did not run into the “caniuse” error and the OOM crash. However, the build still failed with exit error 134 and directed me to look at documentation for the yarn package.
Here is the output you requested. Thank you again for working with me on this:
(galaxy_env3.7.6) galaxy@lenovoserver:~/galaxy$ source .venv/bin/activate
(.venv) (galaxy_env3.7.6) galaxy@lenovoserver:~/galaxy$ source .venv/bin/activate release_23.0
(.venv) (galaxy_env3.7.6) galaxy@lenovoserver:~/galaxy$ which yarn release_23.0
/home/galaxy/galaxy/.venv/bin/yarn
(.venv) (galaxy_env3.7.6) galaxy@lenovoserver:~/galaxy$ which node release_23.0
/home/galaxy/galaxy/.venv/bin/node
(.venv) (galaxy_env3.7.6) galaxy@lenovoserver:~/galaxy$ node --version release_23.0
v18.12.1
(.venv) (galaxy_env3.7.6) galaxy@lenovoserver:~/galaxy$ cd client
(.venv) (galaxy_env3.7.6) galaxy@lenovoserver:~/galaxy/client$ yarn install release_23.0
yarn install v1.22.19
error `install` has been replaced with `add` to add new dependencies. Run "yarn add release_23.0" instead.
info Visit https://yarnpkg.com/en/docs/cli/install for documentation about this command.
(.venv) (galaxy_env3.7.6) galaxy@lenovoserver:~/galaxy/client$ yarn add release_23.0
yarn add v1.22.19
[1/4] Resolving packages...
warning Resolution field "chokidar@3.5.3" is incompatible with requested version "chokidar@^2.0.0"
error An unexpected error occurred: "https://registry.yarnpkg.com/release_23.0: Not found".
info If you think this is a bug, please open a bug report with the information provided in "/home/galaxy/galaxy/client/yarn-error.log".
info Visit https://yarnpkg.com/en/docs/cli/add for documentation about this command.
(.venv) (galaxy_env3.7.6) galaxy@lenovoserver:~/galaxy/client$