scarletblizzard / yadena

Yet Another De Novo Assembler (not finished)

YADeNA

Yet Another De Novo Assembler

Contributing

1. Fork and clone the repository
2. Do your changes
3. Install conda
4. Add bioconda channel:

   conda config --add channels defaults
   conda config --add channels bioconda
   conda config --add channels conda-forge
   conda config --set channel_priority strict
   

5. Create conda environment and install dependencies from the environment.yml file:

   conda env create -n YADeNA -f environment.yml
   

6. Extract out_dir.zip into test_data/ OR
   1. Put FASTA file with reference genome into test_data/ directory
   2. Install ART
   3. Run simulate_data.sh
7. Activate the environment:

   conda activate YADeNA
   

8. Make your changes and, if necessary, install or remove packages using conda
9. Test the program:

   python test_assembler.py
   

   Or run it directly with necessary arguments:

   python assembler.py ...
   

10. Before committing, if you installed or removed packages, run the command

    conda env export > environment.yml
    

11. Commit, push and do a pull request