mirand863 / ganon_cami2

Repository containing detailed installation instructions for ganon with cami2 datasets

ganon_cami2

Repository containing detailed installation instructions for ganon and how to run it with the CAMI2 datasets

Dependency

• Anaconda or Miniconda with python 3.7

Installation with conda

Creating a new conda environment

conda create -n ganon

Activating the environment

conda activate ganon

Adding required channels

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

Installing ganon

conda install ganon=0.1.4

Installing Snakemake

conda install -c bioconda snakemake=5.7.0

Installing Oracle Java

conda install -c gtcg oraclejdk

Downloading CAMI Client

The following commands will be run on folder "/mnt/files/ganon", but it can be changed accordingly

mkdir /mnt/files/ganon
cd /mnt/files/ganon
wget -O camiClient.jar https://data.cami-challenge.org/camiClient.jar

Downloading Datasets

You need to download the marine and strain madness private linkfiles and save them with the names "marine.linkfile" and "strain-madness.linkfile", respectively. Afterwards, run the following commands to download all the required datasets:

wget https://raw.githubusercontent.com/mirand863/ganon_cami2/master/download-datasets.sh
chmod +x download-datasets.sh
./download-datasets.sh

Marine Dataset

Creating config file

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

Downloading and running workflow with snakemake

wget -O Snakefile https://raw.githubusercontent.com/mirand863/ganon_cami2/master/Snakefile
snakemake -s Snakefile --configfile config.yaml -kpr --cores 56 > marine.log

Strain Madness Dataset

Creating config file

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

Downloading and running workflow with snakemake

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