created new branch for sarcoma data

Author: sgosline

build/sarcpdo/README.md

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+# Sarcoma Organoid Dataset
+
+This dataset comes from a [recent publication](https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(24)00296-0?uuid=uuid%3Abb17ce2a-7cc0-48bd-a56d-3bc46a4d5541) with over 100 organoids
+from patient sarcomas. 
+
+## Samples
+
+The sample information is contained in [this synapse
+table](https://www.synapse.org/Synapse:syn61894699/tables/)
+
+
+
+## Omics data
+
+## Drug information
+
+## Experimental measurements

build/sarcpdo/build_drugs.sh

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+#!/bin/bash
+set -euo pipefail
+
+trap 'echo "Error on or near line $LINENO while executing: $BASH_COMMAND"; exit 1' ERR
+
+echo "Running script with token and drugFile $1"
+
+
+echo "Running build_drug_desc.py..."
+#python build_drug_desc.py --drugtable /tmp/beataml_drugs.tsv --desctable /tmp/beataml_drug_descriptors.tsv.gz

build/sarcpdo/build_exp.sh

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+#!/bin/bash
+set -euo pipefail
+
+trap 'echo "Error on or near line $LINENO while executing: $BASH_COMMAND"; exit 1' ERR
+
+echo "Running script with token and curSamples $1 and drugFile $2."
+

build/sarcpdo/build_omics.sh

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+#!/bin/bash
+set -euo pipefail
+
+trap 'echo "Error on or near line $LINENO while executing: $BASH_COMMAND"; exit 1' ERR
+
+echo "Running script with token, curSamples $2, and genes $1."
+

build/sarcpdo/build_samples.sh

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+#!/bin/bash
+set -euo pipefail
+
+trap 'echo "Error on or near line $LINENO while executing: $BASH_COMMAND"; exit 1' ERR
+
+echo ""
+

build/sarcpdo/requirements.txt

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+pandas
+wget==3.2
+requests
+synapseclient
+argparse
+numpy==1.26.4
+openpyxl
+matplotlib
+scikit-learn
+mordredcommunity
+rdkit