Add the execution of exp design loading script to local DB population

ebi-gene-expression-group · Nov 8, 2023 · 778ec3c · 778ec3c
1 parent fc8e641
commit 778ec3c
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/docker/prepare-dev-environment/postgres/docker-compose.yml b/docker/prepare-dev-environment/postgres/docker-compose.yml
@@ -42,9 +42,13 @@ services:
         cd /root/db-scxa/bin
         export PATH=.:$${PATH}
         export dbConnection=postgresql://${POSTGRES_USER}:${POSTGRES_PASSWORD}@${POSTGRES_HOST}:5432/${POSTGRES_DB}
-          
+        
         for EXP_ID in ${EXP_IDS}
         do
+          EXP_ID=$${EXP_ID} \
+          CONDENSED_SDRF_FILE=/atlas-data/exp/magetab/$${EXP_ID}/$${EXP_ID}.condensed-sdrf.tsv \
+          SDRF_FILE=/atlas-data/exp/magetab/$${EXP_ID}/$${EXP_ID}.sdrf.txt ./load_exp_design.sh
+                
           EXPRESSION_TYPE=aggregated_filtered_normalised_counts \
           EXP_ID=$${EXP_ID} \
           EXPERIMENT_MATRICES_PATH=/atlas-data/exp/magetab/$${EXP_ID} ./load_db_scxa_analytics.sh

diff --git a/docker/prepare-dev-environment/solr/Dockerfile b/docker/prepare-dev-environment/solr/Dockerfile
@@ -15,8 +15,8 @@ RUN mkdir -p /root/bioentity-properties-jsonl
 
 # Clone the necessary repositories
 WORKDIR /root
-RUN git clone --depth 1 https://github.com/ebi-gene-expression-group/index-bioentities.git
+RUN git clone --depth 1 --recurse-submodules https://github.com/ebi-gene-expression-group/index-bioentities.git
 RUN git clone --depth 1 --recurse-submodules https://github.com/ebi-gene-expression-group/atlas-web-bulk.git
-RUN git clone --depth 1 https://github.com/ebi-gene-expression-group/index-scxa.git
+RUN git clone --depth 1 --recurse-submodules https://github.com/ebi-gene-expression-group/index-scxa.git
 
 ENTRYPOINT ["/bin/bash", "-c"]