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tutorial_local_singularity.md

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Tutorial for general UNIX computers with singularity

  1. Git clone this pipeline and move into it.

      $ git clone https://github.com/ENCODE-DCC/chip-seq-pipeline2
  $ cd chip-seq-pipeline2

  2. Download cromwell.

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

  3. Download a SUBSAMPLED paired-end sample of ENCSR936XTK.

      $ wget https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR936XTK/ENCSR936XTK_fastq_subsampled.tar
  $ tar xvf ENCSR936XTK_fastq_subsampled.tar

  4. Download pre-built genome database for hg38.

      $ wget https://storage.googleapis.com/encode-pipeline-genome-data/test_genome_database_hg38_chip.tar
  $ tar xvf test_genome_database_hg38_chip.tar

  5. CHECK YOUR SINGULARITY VERSION FIRST AND UPGRADE IT TO A VERSION >=2.5.2 OR PIPELINE WILL NOT WORK CORRECTLY.

      $ singularity --version

  6. Pull a singularity container for the pipeline. This will pull pipeline's docker container first and build a singularity one on ~/.singularity.

      $ SINGULARITY_PULLFOLDER=~/.singularity singularity pull docker://quay.io/encode-dcc/chip-seq-pipeline:v1.1

  7. Run a pipeline for the test sample.

      $ INPUT=examples/local/ENCSR936XTK_subsampled.json
  $ java -jar -Dconfig.file=backends/backend.conf -Dbackend.default=singularity cromwell-34.jar run chip.wdl -i ${INPUT} -o workflow_opts/singularity.json

  8. It will take about an hour. You will be able to find all outputs on cromwell-executions/chip/[RANDOM_HASH_STRING]/. See output directory structure for details.

  9. See full specification for input JSON file.

  10. IF YOU WANT TO RUN PIPELINES WITH YOUR OWN INPUT DATA/GENOME DATABASE, PLEASE ADD THEIR DIRECTORIES TO workflow_opts/singularity.json. For example, you have input FASTQs on /your/input/fastqs/ and genome database installed on /your/genome/database/ then add /your/ to --bind in singularity_command_options. You can also define multiple directories there. It's comma-separated.

      {
      "default_runtime_attributes" : {
          "singularity_container" : "~/.singularity/atac-seq-pipeline-v1.1.simg",
          "singularity_command_options" : "--bind /your/,YOUR_OWN_DATA_DIR1,YOUR_OWN_DATA_DIR2,..."
      }
  }