Omics Pipe Tutorial – Installation

Before Running Omics Pipe: Configuring Parameters File

Note

Before running omics_pipe, you must configure the parameters file, which is a YAML document. Follow the instructions here: Configuring the parameters file

Running Omics Pipe

When you are ready to run omics pipe, simply type the command:

omics_pipe RNAseq_count_based /path/to/parameter_file.yaml

To run the basic RNAseq_count_based pipeline with your parameter file. Additional usage instructions below and are available by typing omics_pipe –h.:

omics_pipe [-h] [--custom_script_path CUSTOM_SCRIPT_PATH]
          [--custom_script_name CUSTOM_SCRIPT_NAME]
                          [--compression {gzip, bzip}]
          {RNAseq_Tuxedo, RNAseq_count_based, RNAseq_cancer_report, RNAseq_TCGA, RNAseq_TCGA_counts,
                          Tumorseq_MUTECT, miRNAseq_count_based, miRNAseq_tuxedo, WES_GATK, WGS_GATK, SomaticInDels, ChIPseq_MACS, ChIPseq_HOMER,  custom}
          parameter_file

If your .fastq files are compressed, please use the compression option and indicate the type of compression used for your files. Currently supported compression types are gzip and bzip.

Running Omics Pipe with the Test Data and Parameters

To run Omics Pipe with the test parameter files and data, type the commands below to run each pipeline.

Note

Replace the ~ with the path to your Omics Pipe installation.

RNA-seq (Tuxedo):

omics_pipe RNAseq_Tuxedo ~/tests/test_params_RNAseq_Tuxedo.yaml

RNA-seq(Anders 2013):

omics_pipe RNAseq_count_based ~/tests/test_params_RNAseq_counts.yaml

Whole Exome Sequencing (GATK):

omics_pipe WES_GATK ~/tests/test_params_WES_GATK.yaml

Whole Genome Sequencing (GATK):

omics_pipe WGS_GATK ~/tests/test_params_WGS_GATK.yaml

Whole Genome Sequencing (MUTECT):

omics_pipe Tumorseq_MUTECT ~/tests/test_params_MUTECT.yaml

ChIP-seq (MACS):

omics_pipe ChIPseq_MACS ~/tests/test_params_MACS.yaml

ChIP-seq (HOMER):

omics_pipe ChIPseq_HOMER ~/tests/test_params_HOMER.yaml

Breast Cancer Personalized Genomics Report- RNAseq:

omics_pipe RNAseq_cancer_report ~/tests/test_params_RNAseq_cancer.yaml

TCGA Reanalysis Pipeline - RNAseq:

omics_pipe RNAseq_TCGA ~/tests/test_params_RNAseq_TCGA.yaml

TCGA Reanalysis Pipeline - RNAseq Counts:

omics_pipe RNAseq_TCGA_counts ~/tests/test_params_RNAseq_TCGA_counts.yaml

miRNAseq Counts (Anders 2013):

omics_pipe miRNAseq_count_based ~/tests/test_params_miRNAseq_counts.yaml

miRNAseq (Tuxedo):

omics_pipe miRNAseq_tuxedo ~/tests/test_params_miRNAseq_Tuxedo.yaml