v1.3.1_Installation

Installation on Flamingo, the GR's computing cluster

Installation of the pipeline

No installation of the pipeline is required. Everything is downloaded, unzipped and installed for you.

Installation of the working environment

No installation of the pipeline is required. Everything is installed for you.

source /mnt/beegfs02/software/recherche/miniconda/25.1.1/etc/profile.d/conda.sh
conda activate /mnt/beegfs02/pipelines/bigr_single-cell/1.3.1/envs/compiled_conda/snakemake
module load singularity-ce/4.2.2-ce

The conda environment contains:

• python (version 3.8.5)
• snakemake (version 5.32.2)
• singularity (version 3.6.3)

It is possible to re-create this environment with conda by:

conda env create -f /mnt/beegfs02/pipelines/bigr_single-cell/1.3.1/envs/conda/snakemake.yaml --prefix="/mnt/beegfs02/pipelines/bigr_single-cell/1.3.1/envs/compiled_conda/snakemake"

Singularity is not in this conda environment because of a namespace issue for slurm, but singularity is available by module load.

Manual installation on your local machine

Installation of the pipeline

To download this workflow:

1. install git (see: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git)
2. git clone https://github.com/gustaveroussy/single-cell.git
3. go in single-cell/resources/WHITELISTS/ and unzip the 3M-february-2018.txt.gz file:

        cd single-cell/resources/WHITELISTS/
        gunzip 3M-february-2018.txt.gz

4. download singularity environments:

        cd  ../../envs/singularity/ #from WHITELISTS folder
        wget "https://zenodo.org/record/5769147/files/single_cell.simg?download=1"
        wget "https://zenodo.org/record/5769147/files/single_cell_DE.simg?download=1"
        wget "https://zenodo.org/record/5769147/files/single_cell_integration.simg?download=1"
        wget "https://zenodo.org/record/5769147/files/single_cell_oldcerebro.simg?download=1"
        wget "https://zenodo.org/record/5769147/files/single_cell_TCR_BCR.simg?download=1"

Installation of the working environment

You need a working environment with:

• python (version 3.8.5)
• snakemake (version 5.32.2)
• singularity (version 3.6.3)

It is possible to create this environment with conda:

1. install conda (see: https://conda.io/projects/conda/en/latest/user-guide/install/index.html)
2. install the environment by: conda env create -f /mnt/beegfs02/pipelines/bigr_single-cell/1.3.1/envs/conda/single-cell_user_local.yaml -n <MyNameEnvir>

To activate the complete environnement:

conda activate <MyNameEnvir>