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2) Snippy
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2) Snippy
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#Snippy seems to have a few bugs on the MacOS version because of the recent updates
#A potential solution is to use Snippy on a Linux based OS instead
#Another potential solution is to use Snippy on Galaxy Bioinformatics
#Attempting to troubleshoot Snippy on Mac OS
#Install
brew install brewsci/bio/snippy
#Template
snippy [options] --outdir <dir> --ref <ref> --R1 <R1.fq.gz> --R2 <R2.fq.gz>
snippy --force --cleanup --outdir {output[0]} --ref {params.ref} --R1 {input[0]} --R2 {input[1]}
#Troubleshoot 1
#Note: The freebayes in snippy is broken
#Freebayes needs to be deleted from Darwin and Linux folders and reinstalled with brew
brew install freebayes
#Troubleshoot 2
#Note: Python 3 is not compatible with Snippy
#Python needs to be systematically downgraded to Python 2.7
brew install python@2
pip install pyenv
pyenv install 2.7.9
python --version
#Also need to find Python in system
which python
#This outputs the folder that the Python is located in
#Delete the entire Python framework
#Samples code that should work with troubleshooting and patches
snippy --force --cleanup --outdir ERR015582_output --ref Mafricanum.gbff --R1 ERR015582_out.R1.fastq.gz --R2 ERR015582_out.R2.fastq.gz