Troubleshooting installation of Clipper 1.2.1

Recently we've been made aware of some issues regarding installation of older Clipper packages. Below is a workaround which may be useful for installing Clipper (1.2.1).

1. create conda environment using [this file].(https://raw.githubusercontent.com/YeoLab/clipper/5a6c49792887b4cfd62fe579bd5946df4ebc62f6/environment.yml) Note, you will need to delete/remove these lines from the file:

  - pip:
    - clipper==0.2.0
    - htseq==0.12.4
prefix: /home/hermuba/anaconda3/envs/clipper

2. download https://github.com/YeoLab/clipper/archive/1.2.1.tar.gz, gunzip & tar -xvf
3. remove random “sc” line from readsToWiggle.pyx file (it’s in clipper 1.2.1 but not 1.2, line ~80)
4. remove GMM class from src/call_peak.py
5. python setup.py install
6. remove readsToWiggle.c file from src directory
7. works!