installation issues

[janursa]

Installation issues encountered by Marco

• (minor) when installing openjdk with homebrew for Mac as described in the openproblems documentation there is another step for me required to link it correctly which is not mentioned sudo ln -sfn /opt/homebrew/opt/openjdk\@11/libexec/openjdk.jdk /Library/Java/JavaVirtualMachines/openjdk.jdk

• when cloning the repository, the "common" submodule doesnt get cloned. So instead I would put the following command in the readme, that automatically also clones the submodules: git clone git@github.com:openproblems-bio/task_grn_inference.git --recurse-submodules

• To download the ressource, the aws CLI tool needs to be installed, this was not mentioned before. Here are the lines of code to install it: curl "https://awscli.amazonaws.com/AWSCLIV2.pkg" -o "AWSCLIV2.pkg" sudo installer -pkg AWSCLIV2.pkg -target /

[janursa]

@rcannood how can we fix these? especially the second one looks quite odd to me.
about the aws, currently we are doing this:

aws s3 sync  s3://openproblems-data/resources/grn/grn_benchmark resources/grn_benchmark --delete --no-sign-request
aws s3 sync  s3://openproblems-data/resources/grn/grn_models resources/grn_models --delete --no-sign-request

which needs to be embedded in common/scripts/sync_resources to avoid aws installation. no?

[rcannood]

@rcannood how can we fix these? especially the second one looks quite odd to me. about the aws, currently we are doing this:

aws s3 sync  s3://openproblems-data/resources/grn/grn_benchmark resources/grn_benchmark --delete --no-sign-request
aws s3 sync  s3://openproblems-data/resources/grn/grn_models resources/grn_models --delete --no-sign-request

which needs to be embedded in common/scripts/sync_resources to avoid aws installation. no?

You store the paths that need to be synced in the _viash.yaml config under section .info.test_resources and run common/scripts/sync_resources.