diff --git a/Dockerfile b/Dockerfile
index faeba79..8c978e8 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -4,12 +4,12 @@ RUN apt-get update && apt-get upgrade -y && apt-get install -y git curl
 
 WORKDIR /code
 
-RUN git clone https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations.git
+RUN git clone https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations.git && \
+    git clone https://github.com/ScilifelabDataCentre/pathogens-portal-scripts.git
 
 COPY *.sh *.py requirements.txt /code/
 
-RUN pip install -r requirements.txt
-
-RUN mkdir output
+RUN pip install -r requirements.txt && \
+    mkdir output
 
 CMD ["/code/all.sh"]
diff --git a/runner_daily.sh b/runner_daily.sh
index d82c0af..bf473ce 100755
--- a/runner_daily.sh
+++ b/runner_daily.sh
@@ -1,3 +1,5 @@
 export CODE_PATH=/code
 
 python "$CODE_PATH"/slack_figshare.py
+
+PYTHONPATH="$CODE_PATH"/pathogens-portal-scripts/EBI_indexing python "$CODE_PATH"/pathogens-portal-scripts/EBI_indexing/update_index_json.py