updated concentrations for MPNS

Author: sgosline

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"]
+VOLUME ["/tmp"]

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,

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