fixed workflows

Author: vr1087

CMakeLists.txt

@@ -5,9 +5,11 @@ FROM ubuntu:22.04 AS builder
 
 # 1) Install build tools, CMake, Git, Python headers, and pip
 RUN apt-get update && apt-get install -y \
+    autoconf \
     build-essential \
     cmake \
     git \
+    libcurl4-openssl-dev \
     python3-dev \
     python3-pip \
  && rm -rf /var/lib/apt/lists/*
@@ -65,8 +67,8 @@ RUN pip3 install pytest
 RUN pytest -q /app/tests/python/test_cli.py
 
 # 4) Verify the binaries are on PATH (just a check; you can remove)
-RUN which aligncount_cpp && which aligncount
+RUN which Aligncount && which aligncount_wrapper
 
 # Final entrypoint: run the Python wrapper by default
-ENTRYPOINT ["aligncount"]
+ENTRYPOINT ["aligncount_wrapper"]
 CMD ["--help"]

Dockerfile

@@ -21,24 +21,24 @@ def main():
     sub = parser.add_subparsers(dest="cmd", required=True)
 
     c1 = sub.add_parser("count-mapped")
-    c1.add_argument("-i", "--input", required=True)
+    c1.add_argument("-a", "--alignments", required=True)
 
     c2 = sub.add_parser("count-unmapped")
-    c2.add_argument("-i", "--input", required=True)
+    c2.add_argument("-a", "--alignments", required=True)
 
     args = parser.parse_args()
-    sam_path = Path(args.input)
+    sam_path = Path(args.alignments)
     if not sam_path.exists():
-        print(f"Error: input file '{args.input}' does not exist.", file=sys.stderr)
+        print(f"Error: input file '{args.alignments}' does not exist.", file=sys.stderr)
         sys.exit(1)
 
     try:
-        raw = subprocess.check_output(["aligncount_cpp", args.input])
+        raw = subprocess.check_output(["Aligncount", "-a", args.alignments])
     except FileNotFoundError:
-        print("Error: C++ binary 'aligncount_cpp' not found in PATH.", file=sys.stderr)
+        print("Error: C++ binary 'Aligncount' not found in PATH.", file=sys.stderr)
         sys.exit(1)
     except subprocess.CalledProcessError as e:
-        print(f"Error: 'aligncount_cpp' failed (exit {e.returncode}).", file=sys.stderr)
+        print(f"Error: 'Aligncount' failed (exit {e.returncode}).", file=sys.stderr)
         sys.exit(e.returncode)
 
     # Use our new helper to produce the final string to print

cli/entrypoint.py

@@ -77,7 +77,7 @@ outputs:
   # ---------------------------------------------------------
   # Output #2: Noarch Python wrapper (aligncount_demo)
   # ---------------------------------------------------------
-  - name: Aligncount_wrapper
+  - name: aligncount_wrapper
     build:
       noarch: python
       script: |

conda-recipe/meta.yaml

@@ -1,12 +1,12 @@
 [metadata]
 name = aligncount
 version = 0.2.0
-description = Aligncount tool
+description = Aligncount wrapper tool
 
 [options]
 packages = find:
 python_requires = >=3.9,<3.14
 
 [options.entry_points]
 console_scripts =
-    aligncount = cli.entrypoint:main
+    aligncount_wrapper = cli.entrypoint:main