Setup

Biologists and bioinformaticians often struggle with software installation. To avoid this issue, we have containerized all the software environments in an Apptainer/Singularity image. This image, along with all the required scripts, can be cloned from our Methylator GitHub repository, available here. If you're using the Jupyter Hub on IFB, you can open a Terminal by clicking on the corresponding icon.

jupyterHub

Before clonning Methylator, go to your project using the cd command.

[username @ cpu-node-12 ]$ cd /shared/projects/YourProjectName

Now you can clone the repository (use -b v0.1 to specify the version).

[username@clust-slurm-client YourProjectName]$ git clone git@github.com:parisepigenetics/WGBSflow.git
Cloning into 'Methylator'...
remote: Enumerating objects: 670, done.
remote: Counting objects: 100% (42/42), done.
remote: Compressing objects: 100% (41/41), done.
remote: Total 670 (delta 1), reused 31 (delta 1), pack-reused 628
Receiving objects: 100% (670/670), 999.24 MiB | 32.76 MiB/s, done.
Resolving deltas: 100% (315/315), done.
Checking out files: 100% (84/84), done.

Enter Methylator directory (cd) and look at the files using tree or ls.

[username@clust-slurm-client YourProjectName]$ cd Methylator
[username@clust-slurm-client Methylator]$ tree -L 2
.
├── configs
│   ├── cluster_config_ifb.yaml
│   ├── cluster_config_ipop.yaml
│   ├── cluster_config.yaml
│   ├── config_nanopore.yaml
│   ├── config_wgbs.yaml
│   ├── metadata_annot.tsv
│   └── metadata.tsv
├── LICENSE
├── my_bank
├── README.md
├── scripts
│   ├── Annotatr.R
│   ├── build_DAG_graphes.sh
│   ├── check_config_path.py
│   ├── colors.yaml
│   ├── DMR.Rmd
│   ├── edc_workflows.py
│   ├── edmr.R
│   ├── final_report_comp.Rmd
│   ├── final_report.Rmd
│   ├── getquota2.sh
│   ├── images
│   ├── main_cluster.py
│   ├── MKit_BedgraphDiff.R
│   ├── MKit_Bedgraph.R
│   ├── MKit_BSMAP.R
│   ├── MKit_diff_bed.R
│   ├── Mkit_differential.Rmd
│   ├── MKit_diff_fig.R
│   ├── MKit_Exploration_all.Rmd
│   ├── MKit_Exploration.Rmd
│   ├── MKit_prep_differential.R
│   ├── MKit_prep_nanopore.R
│   ├── MKit_prep_WGBS.R
│   ├── parse_yaml.sh
│   ├── parsinglog_flow.py
│   ├── parsinglog.py
│   ├── reporting.py
│   ├── run_rule.sh
│   ├── test_bam.R
│   └── Unlock.sh
├── TestDataset
│   ├── bam_nanopore
│   ├── configs
│   ├── fastq
│   └── my_bank
├── WGBSworkflow.sh
└── workflow
    ├── config_main_schema.yaml
    ├── config_mapping_schema.yaml
    ├── config_methylator_schema.yaml
    ├── config_QC_schema.yaml
    ├── config_trim_schema.yaml
    ├── differential.rules
    ├── exploration.rules
    ├── fastq_dump_QC.rules
    ├── mapping.rules
    ├── nanopore.yml
    ├── report.rules
    ├── samples.schema.yaml
    ├── Singularity_ncbi
    ├── trim.rules
    └── wgbsflow.yaml