From 778ec3cc29c8abd66d9cc6f62a47dc77b0a880b8 Mon Sep 17 00:00:00 2001 From: Karoly Erdos Date: Wed, 8 Nov 2023 15:40:53 +0000 Subject: [PATCH] Add the execution of exp design loading script to local DB population --- docker/prepare-dev-environment/postgres/docker-compose.yml | 6 +++++- docker/prepare-dev-environment/solr/Dockerfile | 4 ++-- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/docker/prepare-dev-environment/postgres/docker-compose.yml b/docker/prepare-dev-environment/postgres/docker-compose.yml index 6b1d203c9..97c5ba1a6 100644 --- 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 index d1b55c12f..5fbdc7f33 100644 --- 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"]