Open alondhe opened 8 months ago
Just wanted to make a note about running Strategus on Broadsea since I've spent some time to get this working and wanted to get some feedback on how to potentially share this work with the community.
Some notes on what I've done thus far:
remotes::install_github("OHDSI/Strategus", ref="develop")
(using develop as it can now detect module instantiation problems)ENV INSTATIATED_MODULES_FOLDER="/home/ohdsi/strategus/modules"
RUN R <<EOF
... Contents of the Execute Strategus on Eunomia go here ...
EOF
We may be able to just run Strategus::ensureAllModulesInstantiated with the test analysisSpecification bundled with Strategus but thought running the full study may be better to verify the setup is complete and in good working order.
keyring
, xml2
and when using SqlLite
which are all core packages at the moment. Tagging @leeevans for awareness and input.
I wonder if using a multi-stage build would be a way to handle the libsecret-1-0, libsodium23, libxml2, libglpk-dev dependencies. Are they needed in building or are they continually used by Strategus @anthonysena?
I wonder if using a multi-stage build would be a way to handle the libsecret-1-0, libsodium23, libxml2, libglpk-dev dependencies. Are they needed in building or are they continually used by Strategus @anthonysena?
At the moment, these are used by Strategus when executing. The reason for this is that each module in Strategus will use the keyring
package to access a secure store with credentials. We're considering the elimination of using keyring
in Strategus to simplify things and to eliminate these types of OS dependencies.
I wonder if using a multi-stage build would be a way to handle the libsecret-1-0, libsodium23, libxml2, libglpk-dev dependencies. Are they needed in building or are they continually used by Strategus @anthonysena?
At the moment, these are used by Strategus when executing. The reason for this is that each module in Strategus will use the
keyring
package to access a secure store with credentials. We're considering the elimination of usingkeyring
in Strategus to simplify things and to eliminate these types of OS dependencies.
r-wasm has a multi-stage build approach with keyring that may be worth checking out. The foundational (building) image is flang-wasm Dockerfile which includes Ubuntu and dependencies. That image is then referenced by the webr Dockerfile which is finally cleaned and layers squashed.
https://github.com/OHDSI/Strategus/issues/97