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

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 by:

source /mnt/beegfs/software/conda/etc/profile.d/conda.sh
conda env create -f /mnt/beegfs/pipelines/single-cell/<version>/envs/conda/single-cell_user.yaml --prefix="<path/MyNameEnvir>"

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

To activate the complete environnement:

source /mnt/beegfs/software/conda/etc/profile.d/conda.sh
conda activate <path/MyNameEnvir>
module load singularity

Manual installation on your local machine

Installation of the pipeline

To download this workflow you can use 2 methods:

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. donwload 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"

Or:

1. download this workflow .
2. unzip the dowloaded file
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. donwload 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"

Note: you can also recompile singularity image with singularity tool (singularity can be installed thanks to the "Installation of working environment" next section):

        cd  ../../envs/singularity/ #from WHITELISTS folder
        singularity build single_cell.simg single_cell.def
        singularity build single_cell_TCR_BCR.simg single_cell_TCR_BCR.def
        singularity build single_cell_oldcerebro.simg single_cell_oldcerebro.def

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/beegfs/pipelines/single-cell/envs/conda/single-cell_user_local.yaml -n <MyNameEnvir>

To activate the complete environnement:

conda activate <MyNameEnvir>