Repository containing detailed installation instructions for ganon and how to run it with the CAMI2 datasets
- Anaconda or Miniconda with python 3.7
conda create -n ganon
conda activate ganon
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda install ganon=0.1.4
conda install -c bioconda snakemake=5.7.0
conda install -c gtcg oraclejdk
mkdir /mnt/files/ganon
cd /mnt/files/ganon
wget -O camiClient.jar https://data.cami-challenge.org/camiClient.jar
wget https://raw.githubusercontent.com/mirand863/ganon_cami2/master/download-datasets.sh
chmod +x download-datasets.sh
./download-datasets.sh
cd marine
wget -O create-config.sh https://raw.githubusercontent.com/mirand863/ganon_cami2/master/create-config-marine.sh
chmod +x create-config.sh
./create-config.sh > config.yaml
wget -O Snakefile https://raw.githubusercontent.com/mirand863/ganon_cami2/master/Snakefile
snakemake -s Snakefile --configfile config.yaml -kpr --cores 56 > marine.log
cd strain-madness
wget -O create-config.sh https://raw.githubusercontent.com/mirand863/ganon_cami2/master/create-config-strain-madness.sh
chmod +x create-config.sh
./create-config.sh > config.yaml
wget -O Snakefile https://raw.githubusercontent.com/mirand863/ganon_cami2/master/Snakefile-Strain-Madness
snakemake -s Snakefile --configfile config.yaml -kpr --cores 56 > strain-madness.log