Merge pull request #31 from ScilifelabDataCentre/ebi_index

Add EBI index updater
ScilifelabDataCentre · Apr 15, 2024 · 987e66b · 987e66b
2 parents 2749d9f + eebdf40
commit 987e66b
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diff --git 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
@@ -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