Made final changes so this is ready for build process

Author: jjacobson95

build/build_all.py

@@ -40,7 +40,7 @@ def main():
     parser.add_argument('--figshare', action='store_true', help="Upload all local data to Figshare. FIGSHARE_TOKEN must be set in local environment.")
     parser.add_argument('--all',dest='all',default=False,action='store_true', help="Run all data build commands. This includes docker, samples, omics, drugs, exp arguments. This does not run the validate or figshare commands")
     parser.add_argument('--high_mem',dest='high_mem',default=False,action='store_true',help = "If you have 32 or more CPUs, this option is recommended. It will run many code portions in parallel. If you don't have enough memory, this will cause a run failure.")
-    parser.add_argument('--dataset',dest='datasets',default='broad_sanger,hcmi,beataml,cptac,mpnst,mpnstpdx,pancpdo,bladderpdo,sarcpdo,liverpdo',help='Datasets to process. Defaults to all available.')
+    parser.add_argument('--dataset',dest='datasets',default='broad_sanger,hcmi,beataml,cptac,pancpdo,bladderpdo,sarcpdo,liverpdo,mpnst',help='Datasets to process. Defaults to all available.')
     parser.add_argument('--version', type=str, required=False, help='Version number for the Figshare upload title (e.g., "0.1.29"). This is required for Figshare upload. This must be a higher version than previously published versions.')
     parser.add_argument('--github-username', type=str, required=False, help='GitHub username for the repository.')
     parser.add_argument('--github-email', type=str, required=False, help='GitHub email for the repository.')
@@ -119,7 +119,6 @@ def process_docker(datasets):
             'hcmi': ['hcmi'],
             'beataml': ['beataml'],
             'mpnst': ['mpnst'],
-            'mpnstpdx': ['mpnstpdx'],
             'pancpdo': ['pancpdo'],
             'bladderpdo': ['bladderpdo'],
             'sarcpdo': ['sarcpdo'],
@@ -410,7 +409,7 @@ def get_latest_commit_hash(owner, repo, branch='main'):
     # if args.figshare or args.validate:
         # FigShare File Prefixes:
 
-        prefixes = ['beataml', 'hcmi', 'cptac', 'mpnst', 'mpnstpdx', 'pancpdo', 'bladderpdo','sarcpdo', 'genes', 'drugs', 'liverpdo']
+        prefixes = ['beataml', 'hcmi', 'cptac', 'pancpdo', 'bladderpdo','sarcpdo', 'genes', 'drugs', 'liverpdo','mpnst']
         broad_sanger_datasets = ["ccle","ctrpv2","fimm","gdscv1","gdscv2","gcsi","prism","nci60"]
         if "broad_sanger" in datasets:
             prefixes.extend(broad_sanger_datasets)

build/build_dataset.py

@@ -41,7 +41,6 @@ def process_docker(dataset,validate):
         'hcmi': ['hcmi'],
         'beataml': ['beataml'],
         'mpnst': ['mpnst'],
-        'mpnstpdx': ['mpnstpdx'],
         'pancpdo': ['pancpdo'],
         'cptac': ['cptac'],
         'sarcpdo': ['sarcpdo'],
@@ -128,7 +127,6 @@ def process_omics(executor, dataset, should_continue):
         'broad_sanger': ['copy_number', 'mutations', 'proteomics', 'transcriptomics'],
         'cptac': ['copy_number', 'mutations', 'proteomics', 'transcriptomics'],
         'hcmi': ['mutations', 'transcriptomics'],
-        'mpnstpdx':['copy_number', 'mutations', 'proteomics', 'transcriptomics'],
         'sarcpdo': ['mutations', 'transcriptomics'],
         'pancpdo': ['transcriptomics'],
         'bladderpdo': ['copy_number', 'mutations', 'transcriptomics'],