Use docker container for rules that use R #129
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deprecates the Rlib_dir and Rpkg_config parameters and installation code
because mamba env install just uses conda related to https://www.github.com/mamba-org/mamba/issues/633
kelly-sovacool
changed the title
|
test run in progress bash /data/CCBR_Pipeliner/Pipelines/CARLISLE/carlisle-dev-sovacool/carlisle \
--runmode=runtest \
--workdir=/data/sovacoolkl/carlisle_test_129 |
accidentally got switched back to envmodule during a merge
save precious GHA runtime
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Changes
Use a container with R package dependencies already installed rather than install them to a shared library path. Deprecate the
Rlib_dirandRpkg_configoptions. Use one container for the three rules that require R.This also fixes a bug in the driver script that prevented the singularity bind paths from being parsed correctly. With this PR, we can begin containerizing rules one by one.
Issues
PR Checklist
(
Strikethroughany points that are not applicable.)[ ] Update docs if there are any API changes.CHANGELOG.mdwith a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/