Merge pull request #440 from PNNL-CompBio/pancpdo-manifest

Updated manifest and README

Author: jjacobson95

build/pancpdo/README.md

@@ -1,6 +1,32 @@
-## HCMI Data
+## Pancreatic PDO Data
+
+
+Here we will store the scripts required to process the omics data from the
+Genomic Data Commons together with the drug response data. 
+
+The GDC hosts the panc pdo omcis data, so to update we need an
+up-to-date manifest, obtained as follows:
+
+
+1. Navigate to the [GDC Data
+   Portal](https://portal.gdc.cancer.gov/analysis_page?app=Projects),
+   and select 'ORGANOID-PANCREATIC'
+2. Click on the 'Cases' button, and select the download button where
+   it lists the number of files.
+3. This will download the ENTIRE Manifest
+4. Filter the manifest for RNASeq, WGS mutations, and copy number
+   (though i dont think thi dataset has copy number)
+   calls using the following command:
+```
+ cat ~gdc_manifest.2025-07-08.091940.txt | grep 'rna_seq\|md5'
+   | 'grep counts\|md5' | grep 'txt\|maf\|tsv\|md5' > new_manifest.txt
+ cp new_manifest.txt full_manifest.txt
+ 
+```
+
+The other data is stored [on synapse](https://www.synapse.org/Synapse:syn64597875). 
+
 
-Here we will store the scripts required to process the data from the [Human Cancer Models Initiative](https://ocg.cancer.gov/programs/HCMI)
 
 ## Build Docker