Installing GwasQcPipeline

Installing on CGEMS/CCAD

These are the recommended installation instructions for CGEMS/CCAD.

Create a conda environment (python=3.8):

$ module load miniconda/4.8.3
$ conda create -n GwasQcPipeline -y python=3.8 pip
$ conda activate GwasQcPipeline

Install the current release of the GwasQcPipeline:

$ pip install https://github.com/NCI-CGR/GwasQcPipeline/releases/download/v1.8.0-rc3/cgr_gwas_qc-1.8.0-rc3-py3-none-any.whl
$ cgr --help  # Should provide help information for running the GwasQcPipeline.

After the initial installation, to use GwasQcPipeline:

$ module load miniconda/4.8.3
$ conda activate GwasQcPipeline
$ cgr --help

To update the latest version of GwasQcPipeline:

$ module load miniconda/4.8.3
$ conda activate GwasQcPipeline
$ pip install --force-reinstall https://github.com/NCI-CGR/GwasQcPipeline/releases/download/v1.8.0-rc3/cgr_gwas_qc-1.8.0-rc3-py3-none-any.whl
# See https://github.com/NCI-CGR/GwasQcPipeline/releases for a list of releases

Installing on ccad2

Install miniconda and then create a GwasQcPipeline production environment:

$ mkdir /scratch/myfolder/GwasQcPipeline_v1.8.0-rc3
$ cd /scratch/myfolder/GwasQcPipeline_v1.8.0-rc3
$ wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh
$ bash Miniconda3-py39_4.12.0-Linux-x86_64.sh -p /scratch/myfolder/GwasQcPipeline_v1.8.0-rc3/conda -b
$ source conda/bin/activate base
(base) $ conda update -n base -c defaults conda
(base) $ conda install -n base -c conda-forge mamba
(base) $ conda create -n GwasQcPipeline -y python=3.8 pip
(base) $ conda deactivate

Next install the latest version of the GwasQcPipeline environment:

$ source /scratch/myfolder/GwasQcPipeline_v1.8.0-rc3/conda/bin/activate GwasQcPipeline
(GwasQcPipeline) $ pip install https://github.com/NCI-CGR/GwasQcPipeline/releases/download/v1.8.0-rc3/cgr_gwas_qc-1.8.0-rc3-py3-none-any.whl
(GwasQcPipeline) $ cgr --help
(GwasQcPipeline) $ cgr version
v1.8.0-rc3

Installing on NIH Biowulf

Running the workflow on Biowulf requires installing miniconda and mamba. A detailed description is provided on the Biowulf python env website.

$ wget https://repo.anaconda.com/miniconda/Miniconda3-py39_4.11.0-Linux-x86_64.sh

# Start an interactive session to access tmp folder. Otherwise installation will fail.
$ sinteractive --mem=20g --gres=lscratch:20
$ bash Miniconda3-py39_4.11.0-Linux-x86_64.sh -p /<location of miniconda installation>/conda -b
$ source /<location of miniconda installation>/conda/bin/activate base
$ conda update -n base -c defaults conda
$ conda install -n base -c conda-forge mamba
$ conda create -n GwasQcPipeline -y python=3.8 pip
$ conda deactivate

Next install the latest version of the GwasQcPipeline environment:

$ source /<location of miniconda installation>/conda/bin/activate GwasQcPipeline
$ pip install --force-reinstall https://github.com/NCI-CGR/GwasQcPipeline/releases/download/v1.8.0-rc3/cgr_gwas_qc-1.8.0-rc3-py3-none-any.whl
$ cgr --help
$ cgr version

Installing on other systems

The GwasQcPipeline requires conda to run. We suggest you first install Miniconda. Once you have conda installed, you need to create a conda environment and install the GwasQcPipeline.

$ conda create -n GwasQcPipeline -y python=3.8 pip
$ conda activate GwasQcPipeline
$ pip install https://github.com/NCI-CGR/GwasQcPipeline/releases/download/v1.8.0-rc3/cgr_gwas_qc-1.8.0-rc3-py3-none-any.whl
$ cgr --help  # Should provide help information for running the GwasQcPipeline.

To use GwasQcPipeline first activate your conda environment:

$ conda activate GwasQcPipeline
$ cgr --help

And to update:

$ conda activate GwasQcPipeline
$ pip install --force-reinstall https://github.com/NCI-CGR/GwasQcPipeline/releases/download/v1.8.0-rc3/cgr_gwas_qc-1.8.0-rc3-py3-none-any.whl
# See https://github.com/NCI-CGR/GwasQcPipeline/releases for a list of releases