diff --git a/docker/prepare-dev-environment/postgres/docker-compose.yml b/docker/prepare-dev-environment/postgres/docker-compose.yml index 97c5ba1a6..5a7ebe749 100644 --- a/docker/prepare-dev-environment/postgres/docker-compose.yml +++ b/docker/prepare-dev-environment/postgres/docker-compose.yml @@ -45,29 +45,31 @@ services: 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/$${EXP_ID} ./load_db_scxa_analytics.sh if [ "${SCHEMA_VERSION}" = "18" ]; then - EXP_ID=$${EXP_ID} EXPERIMENT_DIMRED_PATH=/atlas-data/exp/magetab/$${EXP_ID} ./load_db_scxa_dimred.sh + EXP_ID=$${EXP_ID} SCRATCH_DIR=/atlas-data/exp/magetab/$${EXP_ID} ./load_db_scxa_dimred.sh else + EXP_ID=$${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 + # Copied from db-scxa/tests/test-dimred-load.sh ls /atlas-data/exp/magetab/$${EXP_ID}/$${EXP_ID}.tsne*.tsv | while read -r l; do - DIMRED_TYPE=tsne - DIMRED_FILE_PATH=$$l - DIMRED_PARAM_JSON='[{"perplexity": '$(echo "$$l" | sed 's/.*[^0-9]\([0-9]*\).tsv/\1/g')'}]' + DIMRED_TYPE=tsne \ + DIMRED_FILE_PATH=$$l \ + DIMRED_PARAM_JSON='[{"perplexity": '$(echo "$$l" | sed 's/.*[^0-9]\([0-9]*\).tsv/\1/g')'}]' \ + SCRATCH_DIR=/atlas-data/exp/magetab/$${EXP_ID} \ load_db_scxa_dimred.sh $${dbConnection} $${EXP_ID} $${DIMRED_TYPE} $${DIMRED_FILE_PATH} "$${DIMRED_PARAM_JSON}" done ls /atlas-data/exp/magetab/$${EXP_ID}/$${EXP_ID}.umap*.tsv | while read -r l; do - DIMRED_TYPE=umap - DIMRED_FILE_PATH=$$l - DIMRED_PARAM_JSON='[{"n_neighbors": '$(echo "$$l" | sed 's/.*[^0-9]\([0-9]*\).tsv/\1/g')'}]' + DIMRED_TYPE=umap \ + DIMRED_FILE_PATH=$$l \ + DIMRED_PARAM_JSON='[{"n_neighbors": '$(echo "$$l" | sed 's/.*[^0-9]\([0-9]*\).tsv/\1/g')'}]' \ + SCRATCH_DIR=/atlas-data/exp/magetab/$${EXP_ID} \ load_db_scxa_dimred.sh $${dbConnection} $${EXP_ID} $${DIMRED_TYPE} $${DIMRED_FILE_PATH} "$${DIMRED_PARAM_JSON}" done fi