diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 55526d6c0e937d37ce4478a6634a0f3c11c561e5..55787280c7e24d6363002bd03f37487e2fc89c60 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,7 +1,7 @@
 
 variables:
   PIP_CACHE_DIR: "$CI_PROJECT_DIR/.cache/pip"
-  PACKAGES_DIR: "$CI_PROJECT_DIR/packages/"
+  PACKAGES_DIR2: "$CI_PROJECT_DIR/packages/"
   OUTPUT_DIR: "$CI_PROJECT_DIR/outputs/"
 #  OUTPUT_DIR: "/storage/app/EWS_prod/regions/EastAfrica/workspace/"
   TEST_WORKSPACE_DIR: "/storage/app/EWS_prod/regions/EastAfrica/test_workspace/"
@@ -41,7 +41,7 @@ stages:
 
       - echo "project dir - " $CI_PROJECT_DIR
       - echo "output dir - " $OUTPUT_DIR
-      - echo "packages dir - " $PACKAGES_DIR
+      - echo "packages dir - " $PACKAGES_DIR22
       - echo "pip dir - " $PIP_CACHE_DIR
       - echo "full-fat run date - " $FULL_FAT_RUN_DATE
       - echo "custom full-fat run date - " $CUSTOM_RUN_DATE
@@ -49,31 +49,31 @@ stages:
       - source /storage/app/miniconda3/bin/activate /storage/app/EWS_prod/envs/conda/py3EWS/
       - pip install coverage
       - python3 -V  # Print out python version for debugging
-      - mkdir -p $PACKAGES_DIR
+      - mkdir -p $PACKAGES_DIR2
       - mkdir -p $OUTPUT_DIR
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-source-generation.git" $PACKAGES_DIR/source_gen
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_plotting.git" $PACKAGES_DIR/plotting
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/flagdir.git" $PACKAGES_DIR/flagdir
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-epimodel.git" $PACKAGES_DIR/epimodel
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-advisory-builder.git" $PACKAGES_DIR/advisory_builder
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_environmental_suitability_v2.git" $PACKAGES_DIR/environmental_suitability
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-postprocessing.git" $PACKAGES_DIR/post_processing
-      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_met_data_extraction.git" $PACKAGES_DIR/met_extractor_v2
-      - flagdir=$PACKAGES_DIR/flagdir
-      - epimodel=$PACKAGES_DIR/epimodel
-      - advisory=$PACKAGES_DIR/advisory_builder
-      - met_processing=$PACKAGES_DIR/met_extractor_v2/met_data_extraction
-      - met_processor=$PACKAGES_DIR/environmental_suitability
-      - met_processor_temp=$PACKAGES_DIR/environmental_suitability/environmental_suitability
-      - plotting=$PACKAGES_DIR/plotting/plotting
-      - post_processing=$PACKAGES_DIR/post_processing/ews_postprocessing
-      - source_gen=$PACKAGES_DIR/source_gen
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-source-generation.git" $PACKAGES_DIR2/source_gen
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_plotting.git" $PACKAGES_DIR2/plotting
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/flagdir.git" $PACKAGES_DIR2/flagdir
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-epimodel.git" $PACKAGES_DIR2/epimodel
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-advisory-builder.git" $PACKAGES_DIR2/advisory_builder
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_environmental_suitability_v2.git" $PACKAGES_DIR2/environmental_suitability
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews-postprocessing.git" $PACKAGES_DIR2/post_processing
+      - git clone "https://nouser:$GROUP_WHEAT_ACCESS_VAR@gitlab.developers.cam.ac.uk/gilligan-epid/wheat-rusts/ews_met_data_extraction.git" $PACKAGES_DIR2/met_extractor_v2
+      - flagdir=$PACKAGES_DIR2/flagdir
+      - epimodel=$PACKAGES_DIR2/epimodel
+      - advisory=$PACKAGES_DIR2/advisory_builder
+      - met_processing=$PACKAGES_DIR2/met_extractor_v2/met_data_extraction
+      - met_processor=$PACKAGES_DIR2/environmental_suitability
+      - met_processor_temp=$PACKAGES_DIR2/environmental_suitability/environmental_suitability
+      - plotting=$PACKAGES_DIR2/plotting/plotting
+      - post_processing=$PACKAGES_DIR2/post_processing/ews_postprocessing
+      - source_gen=$PACKAGES_DIR2/source_gen
       - coordinator=$CI_PROJECT_DIR/coordinator
       - coordinator_tests=$CI_PROJECT_DIR/tests
       - export PYTHONPATH=$PYTHONPATH:$met_processor_temp:$flagdir:$epimodel:$advisory:$met_processing:$met_processor:$plotting:$source_gen:$post_processing:$coordinator:$coordinator_tests
       - echo "pythonpath - " $PYTHONPATH
 
-      - ls $PACKAGES_DIR
+      - ls $PACKAGES_DIR2
 
 half_fat_tests:
   when: manual