diff --git a/concore_cli/commands/run.py b/concore_cli/commands/run.py
index c6aaed2..91a876b 100644
--- a/concore_cli/commands/run.py
+++ b/concore_cli/commands/run.py
@@ -5,10 +5,17 @@
 from rich.panel import Panel
 from rich.progress import Progress, SpinnerColumn, TextColumn
 
+def _find_mkconcore_path():
+    for parent in Path(__file__).resolve().parents:
+        candidate = parent / "mkconcore.py"
+        if candidate.exists():
+            return candidate
+    return None
+
 def run_workflow(workflow_file, source, output, exec_type, auto_build, console):
     workflow_path = Path(workflow_file).resolve()
     source_path = Path(source).resolve()
-    output_path = Path(output)
+    output_path = Path(output).resolve()
     
     if not source_path.exists():
         raise FileNotFoundError(f"Source directory '{source}' not found")
@@ -24,6 +31,10 @@ def run_workflow(workflow_file, source, output, exec_type, auto_build, console):
     console.print(f"[cyan]Type:[/cyan] {exec_type}")
     console.print()
     
+    mkconcore_path = _find_mkconcore_path()
+    if mkconcore_path is None:
+        raise FileNotFoundError("mkconcore.py not found. Please install concore from source.")
+
     with Progress(
         SpinnerColumn(),
         TextColumn("[progress.description]{task.description}"),
@@ -33,7 +44,8 @@ def run_workflow(workflow_file, source, output, exec_type, auto_build, console):
         
         try:
             result = subprocess.run(
-                [sys.executable, 'mkconcore.py', str(workflow_path), str(source_path), str(output_path), exec_type],
+                [sys.executable, str(mkconcore_path), str(workflow_path), str(source_path), str(output_path), exec_type],
+                cwd=mkconcore_path.parent,
                 capture_output=True,
                 text=True,
                 check=True
diff --git a/mkconcore.py b/mkconcore.py
index 10135dc..e630dd9 100644
--- a/mkconcore.py
+++ b/mkconcore.py
@@ -72,11 +72,22 @@
 import copy_with_port_portname
 import numpy as np
 
-MKCONCORE_VER = "22-09-18"
-
-GRAPHML_FILE = sys.argv[1]
-TRIMMED_LOGS = True
-CONCOREPATH = "."
+MKCONCORE_VER = "22-09-18"
+
+SCRIPT_DIR = os.path.dirname(os.path.abspath(__file__))
+
+def _resolve_concore_path():
+    script_concore = os.path.join(SCRIPT_DIR, "concore.py")
+    if os.path.exists(script_concore):
+        return SCRIPT_DIR
+    cwd_concore = os.path.join(os.getcwd(), "concore.py")
+    if os.path.exists(cwd_concore):
+        return os.getcwd()
+    return SCRIPT_DIR
+
+GRAPHML_FILE = sys.argv[1]
+TRIMMED_LOGS = True
+CONCOREPATH = _resolve_concore_path()
 CPPWIN    = "g++"        #Windows C++  6/22/21
 CPPEXE    = "g++"        #Ubuntu/macOS C++  6/22/21
 VWIN      = "iverilog"   #Windows verilog  6/25/21
diff --git a/tests/test_cli.py b/tests/test_cli.py
index af31a36..a90cc3f 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -67,7 +67,22 @@ def test_run_command_missing_source(self):
             result = self.runner.invoke(cli, ['init', 'test-project'])
             result = self.runner.invoke(cli, ['run', 'test-project/workflow.graphml', '--source', 'nonexistent'])
             self.assertNotEqual(result.exit_code, 0)
-    
+
+    def test_run_command_from_project_dir(self):
+        with self.runner.isolated_filesystem(temp_dir=self.temp_dir):
+            result = self.runner.invoke(cli, ['init', 'test-project'])
+            self.assertEqual(result.exit_code, 0)
+
+            result = self.runner.invoke(cli, [
+                'run',
+                'test-project/workflow.graphml',
+                '--source', 'test-project/src',
+                '--output', 'out',
+                '--type', 'posix'
+            ])
+            self.assertEqual(result.exit_code, 0)
+            self.assertTrue(Path('out/src/concore.py').exists())
+
     def test_run_command_existing_output(self):
         with self.runner.isolated_filesystem(temp_dir=self.temp_dir):
             result = self.runner.invoke(cli, ['init', 'test-project'])