Welcome to the documentation for Omics Pipe! Omics pipe is an open-source, modular computational platform that automates �best practice� multi-omics data analysis pipelines published in Nature Protocols and other commonly used pipelines, such as GATK. It currently automates and provides summary reports for two RNA-seq pipelines, variant calling from whole exome sequencing (WES), variant calling and copy number variation analysis from whole genome sequencing (WGS), two ChIP-seq pipelines and a custom RNA-seq pipeline for personalized genomic medicine reporting. It also provides automated support for interacting with the The Cancer Genome Atlas (TCGA) datasets, including automatic download and processing of the samples in this database.
HPC Cluster or AWS Star Cluster
Python 2.6 or newer
Software Dependencies installed as Modules
Reference Databases
Option 1
pip install omics_pipe
Option 2
easy_install omics_pipe
Option 3 -- download/extract the source code
python setup.py install
Option 4 -- install the latest code directly from the repository
pip install -e hg+https://bitbucket.org/sulab/omics_pipe#egg=omics_pipe
Option 5 -- if you do not have administrator privileges
*Step 1: Set up a [Python virtual environment](http://docs.python-guide.org/en/latest/dev/virtualenvs/)
*Step 2: Use one of the Options (1-4) above to install Omics Pipe within your virtual environment.
command-line usage::
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
Current DB Snapshot: snap-2db684e3 (27 Aug 2014)
Current AMI: ami-2b676b6e
Feedback welcome at: [email protected]
Twitter: Kathlessn Fisch: @kathleenfisch Adam Mark: @AdamMaikai
Google Group: https://groups.google.com/forum/#!forum/omics_pipe