backofenlab / casboundary Goto Github PK

Bootstrap: docker
From: mambaorg/micromamba:1.4.9

%files
        ./v1.0.1.zip /opt/                  # Copy latest version from current dir into the container
        ./*.tar /opt/                       # Copy the four '.tar' files from current dir into the container

%post
        apt update -y && apt install zip  -y
        unzip /opt/v1.0.1.zip -d /opt/                            # Unzip Casboundary
        mv /opt/*.tar /opt/Casboundary-1.0.1/                     # Move models into installation path
        cd /opt/Casboundary-1.0.1/                                # Go inside installation path
        chmod +x *.py                                             # Make all py files executable
        tar -xf Cas_HMM.tar                                       # Untar models ...
        tar -xf Gen_HMM.tar
        tar -xf ML_models.tar
        tar -xf Cas_HMM.tar
        micromamba create -f casboundary-env.yml       # Create and solve env
        micromamba clean --all --yes

%environment
        export PATH=/opt/Casboundary-1.0.1:/opt/conda/envs/casboundary-env/bin:$PATH  # Export binary paths to PATH 

%runscript
         python /opt/Casboundary-1.0.1/Casboundary.py "$@"  # Runscript

$ singularity run /home/iferres/singularity/casboundary/casboundary.sif -f dummy.fasta -c complete
Traceback (most recent call last):
  File "/opt/Casboundary-1.0.1/Casboundary.py", line 311, in <module>
    extract_targz(CAS_HMM_TAR_PATH)
  File "/opt/Casboundary-1.0.1/utils.py", line 31, in extract_targz
    raise ValueError(f'{targz_file_path} file not found. You should download it from our Google Drive. See README.md for details.')
ValueError: Cas_HMM.tar.gz file not found. You should download it from our Google Drive. See README.md for details.

Casboundary.py ... --models_dir /path/to/models/ dummy.fasta