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Tutorial for Stanford SCG4 cluster

This tutorial shows how to run pipelines on SCG4. You may need to have a paid account on it because SCG4 does not offer any free of charge SLURM partition. We recommend that free users use Sherlock instead.

All test samples and genome data are shared on Stanford SCG4 cluster based on SLURM. You don't have to download any data for testing our pipeline on it.

  1. SSH to SCG's login node.

    $ ssh login.scg.stanford.edu

  2. Download cromwell on your $HOME directory.

    $ cd 
$ wget https://github.com/broadinstitute/cromwell/releases/download/34/cromwell-34.jar
$ chmod +rx cromwell-34.jar

  3. Git clone this pipeline and move into its directory.

    $ cd
$ git clone https://github.com/ENCODE-DCC/atac-seq-pipeline
$ cd atac-seq-pipeline

Our pipeline supports both Conda and Singularity.

For Conda users

  1. Install Conda dependencies.

    $ module load miniconda/3
$ bash conda/uninstall_dependencies.sh  # to remove any existing pipeline env
$ bash conda/install_dependencies.sh

  2. Run a pipeline for the test sample. You must have a paid account on SCG4.

    $ sbatch --account [YOUR_PAID_ACCOUNT_ON_SCG4] examples/scg/ENCSR356KRQ_subsampled_scg_conda.sh

For singularity users

  1. Run a pipeline for the test sample. You must have a paid account on SCG4. 
    $ sbatch --account [YOUR_PAID_ACCOUNT_ON_SCG4] examples/scg/ENCSR356KRQ_subsampled_scg_singularity.sh

For all users

  1. It will take about an hour. You will be able to find all outputs on cromwell-executions/atac/[RANDOM_HASH_STRING]/. See output directory structure for details. You can monitor your jobs with the following command:

    $ squeue -u $USER

  2. See full specification for input JSON file.

  3. You can resume a failed pipeline from where it left off by using PIPELINE_METADATA(metadata.json) file. This file is created for each pipeline run. See here for details. Once you get a new input JSON file from the resumer, then edit your shell script (examples/scg/ENCSR356KRQ_subsampled_scg_*.sh) to use it INPUT=resume.[FAILED_WORKFLOW_ID].json instead of INPUT=examples/....

For singularity users

  1. IF YOU WANT TO RUN PIPELINES WITH YOUR OWN INPUT DATA/GENOME DATABASE, PLEASE ADD THEIR DIRECTORIES TO workflow_opts/scg.json. For example, you have input FASTQs on /your/input/fastqs/ and genome database installed on /your/genome/database/ then add /your/ to singularity_bindpath. You can also define multiple directories there. It's comma-separated. 
    {
    "default_runtime_attributes" : {
        "singularity_container" : "~/.singularity/atac-seq-pipeline-v1.3.0.simg",
        "singularity_bindpath" : "/reference/ENCODE,/scratch,/srv/gsfs0,YOUR_OWN_DATA_DIR1,YOUR_OWN_DATA_DIR1,..."
    }
}