Conda.md

Conda Environment

1. Download and install conda

Download an an installer for Python v3. (cfCloud requires python=3.7)

distribution	instructions
Anaconda	Current version "Python 3.7 version"
Miniconda	Download the Miniconda3-latest-* installer based on your operating system

Run the installer file. Depends on. your OS. It may be an executable installer or run from the command-line: bash INSTALLER.sh . Please see the instruction provided with the installer.

# Example:
wget https://repo.anaconda.com/archive/Anaconda3-2020.02-Linux-x86_64.sh
bash Anaconda3-2020.02-Linux-x86_64.sh

2. Create a new environment

conda create --name cfcloud python=3.6
conda activate cfcloud
conda info --envs

3. Tool Prerequisites

conda install -c anaconda pandas -y
conda install -c bioconda snakemake -y
conda install -c bioconda bcftools -y
conda install -c bioconda samtools -y
conda install -c bioconda pyvcf -y
conda list
sudo apt install unzip

4. Clone cfCloud

git clone https://github.com/NHLBI-BCB/cfCloud.git
cd cfCloud

5. Install resources

• Bowtie2 Reference Genome
  Can be downloaded from Illumina iGenomes

# e.g. hg19:
cd resources
wget http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz
tar -xzf Homo_sapiens_UCSC_hg19.tar.gz

• SNPs list
  Can be downloaded from Illumina Genotyping Kits

# e.g. Infinium Omni2.5:
cd resurces
unzip InfiniumOmni25.hg19.snps.cleaned.zip

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