Merge pull request #355 from PNNL-CompBio/bladderpdo_docs

Update README.md

Author: sgosline

build/bladderpdo/README.md

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+# Bladder Patient Derived Organoid Dataset
+
+This dataset comes from a [2018 publication](https://www.sciencedirect.com/science/article/pii/S0092867418302976?via%3Dihub) (Lee et. al., 2018) that created several bladder PDO lines from xenografts in mice and performed sequencing and drug experiments. 
+
+## Samples
+
+Sample information can be found on Synapse [here](https://www.synapse.org/Synapse:syn64765486).
+
+## Omics Data
+
+This study had copy number variation, RNA-seq and mutation data that was included. 
+
+Copy number data is available at [this synapse link](https://www.synapse.org/Synapse:syn64765499). Mutation data is available at [this synapse link](https://www.synapse.org/Synapse:syn64765525). RNA-Seq data was acquired from GEO, we used the 'GSE1039990_Normalized_counts.txt.gz' table available on GEO [GSE103990](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103990). 
+
+## 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. 
+
+## 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
+```