#Download the mapping from sample barcodes to uuid
./tcgaImport.py download uuid -o data/tcga_uuid_map

#Determine what is out of date or missing in Synapse 
./synapseCompare_meta.py --project syn2812961 -o to_update.txt

#Go through the files that need updating in to_update.txt
./tcgaImport.py build --rmControl -u data/tcga_uuid_map -w workdir -m mirror --checksum-delete --download --outdir out mdanderson.org_BLCA_MDA_RPPA_Core

#Push the changes to Synapse (this is a dry run, to actually push changes use --push)
./synapseLoad_files.py --project syn2812961 out/

#Merge files into PANCAN files (replace benefactorId with synapse projectId to merge files from and parentId with synapse project Id to upload merged files to.)
python mergeByPlatform.py benefactorId parentId 

#Update the sample summary table
python synapseUpdateSummaryTable.py --project syn2812961 --table syn3281840

# =====
# Get the UCEC clinical matrix
# =====
#
# ./tcgaImport.py -u tcga_uuid_map -w /inside/grotto/tmp -m /inside/grotto/TCGA --outdir ./clin/ -d -r -b nationwidechildrens.org_UCEC_bio
#
#
# =====
# Build Pipeline
# =====
#
# ./build_base.sh
#
# =====
# File upload
# =====
# 
# ./synapseLoad_dirs.py  --project syn1446577 out/ --push
# ./synapseLoad_files.py --project syn1446577 out/ --push
# ./synapseLoad_meta.py --project syn1446577 out/ 
# ./synapseLoad_provenance.py --project syn1446577 out/