Update README.md

Added examples to readme of how to run code to generate bladderpdo datasets from command line.

Author: RubyFore

build/bladderpdo/README.md

@@ -14,4 +14,36 @@ Copy number data is available at [this synapse link](https://www.synapse.org/Syn
 
 ## Drug Dose-Response Experiments
 
-For these data, we had complete drug dose-response data to recalculate curves, available on Synapse in the [Lee Bladder PDO Datasets](https://www.synapse.org/Synapse:syn64765430) folder. 
+For these data, we had complete drug dose-response data to recalculate curves, available on Synapse in the [Lee Bladder PDO Datasets](https://www.synapse.org/Synapse:syn64765430) folder. 
+
+## To Run Code 
+
+### First sample and omics steps are the same, by hand locally or in full build process
+```
+python3 00_createBladderPDOSampleFile.py --token $SYNAPSE_AUTH_TOKEN -p prevSamples
+
+# for mutation data (-m)
+python3 01_createBladderPDOOmicsFiles.py --token $SYNAPSE_AUTH_TOKEN -s curSamples -g genes.csv -m
+# for expressiondata (-e)
+python3 01_createBladderPDOOmicsFiles.py --token $SYNAPSE_AUTH_TOKEN -s curSamples -g genes.csv -e
+# for copynumber (-c)
+python3 01_createBladderPDOOmicsFiles.py --token $SYNAPSE_AUTH_TOKEN -s curSamples -g genes.csv -c
+```
+
+### For drug and experiment steps, command depends on location of helper scripts
+```
+# for running locally (from build directory):
+python3 -m bladderpdo.02_createBladderPDODrugsFile --token $SYNAPSE_AUTH_TOKEN -d prevDrugFilePath -o ./bladderpdo/bladderpdo_drugs.tsv
+# for running in Docker as part of full build
+python3 02_createBladderPDODrugsFile.py --token $SYNAPSE_AUTH_TOKEN -d prevDrugFilePath -o /tmp/bladderpdo_drugs.tsv
+
+# for running locally (from build directory): 
+python3 utils/build_drug_desc.py --drugtable ./bladderpdo/bladderpdo_drugs.tsv --desctable ./bladderpdo/bladderpdo_drug_descriptors.tsv.gz
+# for running in docker as part of full build
+python3 build_drug_desc.py --drugtable /tmp/bladderpdo_drugs.tsv --desctable /tmp/bladderpdo_drug_descriptors.tsv.gz
+
+
+python3 03_createBladderPDOExperimentFile.py --token $SYNAPSE_AUTH_TOKEN --drugfile curDrugFile --curSampleFile curSampleFile --output /tmp/bladderpdo_doserep.tsv
+
+python3 fit_curve.py --input /tmp/bladderpdo_doserep.tsv --output /tmp/bladderpdo_experiments.tsv
+```