The best way to manage the dependency of this repo is through a conda virtual environment. Use the following commands in your terminal
conda create intactness python=3
conda activate intactness
conda install --file requirements.txt
Please check this site for information.
The whole repo is intended to be used as a template folder for reproducible research purpose. Please create a copy of this folder each time your run the pipeline.
The following steps should be taken in order, in the root folder of the project.
- Store the DNA sequences in a FASTA file named "seqs.fasta" in
datafolder - Specify your email address on the 5th line in
intactness/default.cfg conda activate intactnesspython3 -m intactness- The result is in
data/seqs/summary.csv
For advanced users, the settings are stored in intactness/default.cfg.