Requirement¶
Dependencies¶
- Command-line pacakges:
| Python package | Version >= |
|---|---|
| bedtools | 2.26.0 |
- Python package:
| Python package | Version >= |
|---|---|
| colorama | 0.3.7 |
| glmnet_py | 0.1.0b |
| gffutils | 0.8.7.1 |
| matplotlib | 1.5.1 |
| numpy | 1.11.2 |
| pandas | 0.19.2 |
| pybedtools | 0.7.8 |
| pyfiglet | 0.7.5 |
| pysam | 0.9.1.4 |
| scikit_learn | 0.18 |
| scipy | 0.18.1 |
| seaborn | 0.7.0 |
| termcolor | 1.1.0 |
Note: When using pip install scikit-ribo, all the following dependencies will be pulled and installed automatically.
Installation¶
Options¶
There are three options to install Scikit-ribo.
Install Scikit-ribo with pip:
pip install scikit-ribo
Install Scikit-ribo with conda/biocodon:
Coming up
Compile from source:
git clone https://github.com/hanfang/scikit-ribo.git cd scikit-ribo python setup.py install
Test whether the installation is successful¶
Once the installation is successful, you should expect the below if you type:
scikit-ribo-run.py
