diff --git a/build/docker/Dockerfile.mpnst b/build/docker/Dockerfile.mpnst index 93c0bbaa..92fe9c6d 100755 --- a/build/docker/Dockerfile.mpnst +++ b/build/docker/Dockerfile.mpnst @@ -31,7 +31,7 @@ RUN /opt/venv/bin/pip install --upgrade pip # Set environment variables for reticulate ENV RETICULATE_PYTHON="/opt/venv/bin/python3" -ENV PYTHONPATH="${PYTHONPATH}:/app" +ENV PYTHONPATH=/app#"${PYTHONPATH}:/app" WORKDIR /app # Set MPLCONFIGDIR to a writable directory @@ -51,4 +51,4 @@ RUN /opt/venv/bin/pip3 install -r requirements.txt RUN Rscript requirements.r # Set up volume for temporary storage -VOLUME ["/tmp"] \ No newline at end of file +VOLUME ["/tmp"] diff --git a/build/mpnst/03_get_drug_response_data.R b/build/mpnst/03_get_drug_response_data.R index 357eb0aa..8f02ca80 100644 --- a/build/mpnst/03_get_drug_response_data.R +++ b/build/mpnst/03_get_drug_response_data.R @@ -85,7 +85,7 @@ getDrugDataByParent<-function(parid,sampleId){ data <- fread(synGet(x)$path)|> filter(response_type=='percent viability')|> mutate(improve_sample_id=sampleId, - DOSE=exp(dosage)/1000000, ##dosage is log(M), need to move to micromolar + DOSE=(10^dosage)*1000000, ##dosage is log(M), need to move to micromolar GROWTH=response, #/100, source = "NF Data Portal", #CELL = improve_sample_id, diff --git a/build/mpnst/README.md b/build/mpnst/README.md index 13c08454..10d0bcd9 100755 --- a/build/mpnst/README.md +++ b/build/mpnst/README.md @@ -12,7 +12,7 @@ directory. Currently using the test files as input. `mpnst_samples.csv` file. This pulls from the latest synapse project metadata table. ``` - docker run -v $PWD:/tmp -e -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN mpnst sh build_samples.sh /tmp/build/build_test/test_samples.csv + docker run -v $PWD:/tmp -e SYNAPSE_AUTH_TOKEN=$SYNAPSE_AUTH_TOKEN mpnst sh build_samples.sh /tmp/build/build_test/test_samples.csv ``` 3. Pull the data and map it to the samples. This uses the metadata