Osc_bc_rstudio_server streamlined submit.yml.erb

jeff.ohrstrom · June 10, 2022, 1:06am

Also is this file being created somewhere? Every file in the template directory will be copied to $WORKING_DIR.

That’s how I mount configs like the db.conf.

OSC/bc_osc_rstudio_server/blob/1ce2e4fb1ddb25921069a1e31cb3edc02ce90535/template/script.sh.erb#L144


      
          # --contain is used to override the bindpaths specified in OSC's
          # singularity.conf which would otherwise conflict in /etc
          # using --contain requires us to bind mount in addition directories including
          # /dev and /proc
          # optional_tutorial_home_bind is used when include_tutorials to change the home
          # directory to get a clean environment without clobbering files
          SINGULARITYENV_LD_LIBRARY_PATH="$LD_LIBRARY_PATH" \
            singularity run --contain \
           -B $TMPDIR:/tmp \
           -B $WORKING_DIR \
           -B $WORKING_DIR/etc:/etc/rstudio \
           -B /etc/fonts \
           -B /etc/profile \
           -B /etc/profile.d \
           -B /etc/alternatives \
           -B <%= module_dir %> \
           "$RSTUDIO_SERVER_IMAGE" \
           --www-port "${port}" \
           --auth-none 0 \
           --auth-pam-helper-path "${RSTUDIO_AUTH}" \
           --auth-encrypt-password 0 \

Plus, since every file is templated, I can configure the log directory to the effectively the same directory as WORKING_DIR.

github.com

OSC/bc_osc_rstudio_server/blob/1ce2e4fb1ddb25921069a1e31cb3edc02ce90535/template/etc/logging.conf.erb#L4


      
          [*]
          log-level=debug
          logger-type=file
          log-dir=<%= session.staged_root.join('logs') %>

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Osc_bc_rstudio_server streamlined submit.yml.erb

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