Merge pull request #121 from CCBR/fix-reconfig

fix: reconfig needs to use platform-specific configfile

CHANGELOG.md

@@ -4,6 +4,9 @@
 
 - CHARLIE was falsely throwing a file permissions error for tempdir values containing bash variables. (#118, @kelly-sovacool)
 - Singularity bind paths were not being set properly. (#119, @kelly-sovacool)
+- Update docker containers to set `$PYTHONPATH`. (#119, @kelly-sovacool)
+  - Otherwise, this environment variable can be carried over and cause package conflicts when singularity is not run with `-C`.
+- Fix `reconfig` to correctly replace variables in the config file. (#121, @kelly-sovacool)
 
 ## CHARLIE 0.11.0
 

charlie

@@ -294,9 +294,13 @@ function reconfig(){
   # rebuild config file and replace the config.yaml in the WORKDIR
   # this is only for dev purposes when new key-value pairs are being added to the config file
   check_essential_files
-  sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" -e "s/WORKDIR/${WORKDIR//\//\\/}/g" \
-  ${PIPELINE_HOME}/config/config.yaml |\
-  cat - ${PIPELINE_HOME}/config/containers.yaml > $WORKDIR/config.yaml
+  sed -e "s/PIPELINE_HOME/${PIPELINE_HOME//\//\\/}/g" \
+    -e "s/WORKDIR/${WORKDIR//\//\\/}/g" \
+    -e "s/HOST/${HOST}/g" \
+    -e "s/ADDITIVES/${ADDITIVES}/g" \
+    -e "s/VIRUSES/${VIRUSES}/g" \
+    ${PIPELINE_HOME}/config/$PLATFORM/config.yaml |\
+    cat - ${PIPELINE_HOME}/config/containers.yaml > $CONFIGFILE
   echo "$WORKDIR/config.yaml has been updated!"
 }