Add software ABC

Author: mrcela

barrel/worker/src/bioinformatics/software.py

@@ -0,0 +1,40 @@
+import worker
+
+from abc import ABC, abstractproperty
+from dataclasses import dataclass
+from pathlib import Path
+
+
+@dataclass
+class Program(ABC):
+    version: str
+    location: Path
+
+    @abstractproperty
+    def install_command(self) -> str:
+        pass
+
+    @abstractproperty
+    def executable(self) -> Path:
+        pass
+
+    def __post_init__(self):
+        self.installation = self.install()
+
+    def install(self) -> str:
+        command = f"""
+            if [ -d "{self.location}" ]; then exit 0; fi
+            
+            mkdir -p {self.location}
+
+            export TEMPORARY_DIRECTORY=$(mktemp -d)
+            cd $TEMPORARY_DIRECTORY
+
+            {self.install_command}
+
+            rm -r $TEMPORARY_DIRECTORY
+        """
+
+        name = type(self).__name__
+        return worker.execute(command, job_name=f"INSTALL_{name}", vcpu=8, memory=16000)
+