omics_pipe
  • Omics Pipe
    • Introduction
    • Installation
    • Tutorials
    • Online Resources
    • Site Navigation
  • About Omics Pipe
    • Available Pipelines
    • Users
    • Developers
    • Contact
  • Using Omics Pipe
    • Requirements
    • Installation
    • Usage
    • Running Omics Pipe on Amazon Web Services (AWS)
    • Tutorial
    • Version history
    • Documentation
    • Questions
  • OmicsPipe on the Amazon Cloud (AWS EC2) Tutorial
    • Step 1: Create an AWS Account
    • Step 2 (Mac or Linux): Install StarCluster and download config/plugins
    • Step 2 (Windows): Load the the OmicsPipe on AWS docker image on your machine
    • Step 3: Configure StarCluster
    • Step 4: Create AWS Volumes
    • Step 5: Launch the Cluster
    • Step 6: Upload data to the cluster
    • Step 7: Run the test pipelines
    • Step 8: Run the pipelines with your own data
    • Installing extra software
    • To build your own docker image
    • Add storage > 1TB to the cluster using LVM (for advanced users)
    • Add storage > 1TB to the cluster using RAID 0 (for advanced users)
    • Backing up your data to S3
  • Omics Pipe Tutorial
    • Installation
    • Before Running Omics Pipe: Configuring Parameters File
    • Running Omics Pipe
    • Running Omics Pipe with the Test Data and Parameters
    • Running Omics Pipe with your own data
  • Omics Pipe Tutorial – Configuring the Parameter File
    • Example Omics Pipe Parameter File
    • Explanation of Variables in Omics Pipe Parameter File
  • Omics Pipe Tutorial – Creating a Custom Pipeline Script
    • Designing the structure of the pipeline
    • Creating the script
    • Updating your parameters file
  • Omics Pipe Tutorial – Adding a New Module (Tool)
    • 1. Create a Bash script
    • 2. Create a Python module
    • 3. Add custom Python module to your custom pipeline
    • 4. Add new parameters to parameters file
  • Omics Pipe Available Pipelines
    • RNA-seq (Tuxedo)
    • RNA-seq(Anders 2013)
    • Whole Exome Sequencing (GATK)
    • Whole Genome Sequencing (GATK)
    • Whole Genome Sequencing (MUTECT)
    • ChIP-seq (MACS)
    • ChIP-seq (HOMER)
    • Breast Cancer Personalized Genomics Report- RNAseq
    • TCGA Reanalysis Pipeline - RNAseq
    • TCGA Reanalysis Pipeline - RNAseq Counts
    • miRNAseq Counts (Anders 2013)
    • miRNAseq (Tuxedo)
    • All Available Modules
  • Reference Databases Needed
    • All Pipelines
    • Reference Data for Cancer Reporting Scripts (RNAseq cancer, TCGA pipelines)
    • References for Variants (RNA-seq cancer, RNA-seq cancer TCGA, WES and WGS pipelines)
    • WES Pipeline
    • ChIP-seq Pipelines
    • SNPiR Pipelines (RNA-seq cancer and RNA-seq cancer TCGA pipelines)
  • Third Party Software Dependencies
    • R Packages Needed
    • RNA-seq (Tuxedo)
    • RNA-seq (Anders 2013)
    • Whole Exome Sequencing (GATK)
    • Whole Genome Sequencing (GATK)
    • Whole Genome Sequencing (MUTECT)
    • ChIP-seq (MACS)
    • ChIP-seq (HOMER)
    • Breast Cancer Personalized Genomics Report- RNAseq
    • TCGA Reanalysis Pipeline - RNAseq
    • TCGA Reanalysis Pipeline - RNAseq Counts
    • miRNAseq Counts (Anders 2013)
    • miRNAseq (Tuxedo)
  • System Requirements
  • RNA-seq Tuxedo Modules
    • FASTQC
    • TopHat
    • Cufflinks
    • Cuffmerge
    • Cuffmergetocompare
    • Cuffdiff
    • R Summary Report
  • RNA-seq Count Based Modules
    • FASTQC
    • STAR Aligner
    • HTSEQ-count
    • R Summary Report - DESEQ2
  • Breast Cancer Personalized Genomics Report- RNAseq
    • FASTQC
    • STAR Aligner
    • HTSEQ-count
    • RSEQC
    • Fusion Catcher
    • BWA/SNPiR
    • Intogen
    • OncoRep Cancer Report
  • TCGA Reanalysis Pipeline - RNAseq
    • TCGA Download
    • FASTQC
    • STAR Aligner
    • HTSEQ-count
    • RSEQC
    • Fusion Catcher
    • BWA/SNPiR
    • Intogen
    • OncoRep Cancer Report
  • RNA-seq Count Based Modules- TCGA
    • TCGA Download
    • FASTQC
    • STAR Aligner
    • HTSEQ-count
    • R Summary Report - DESEQ2
  • miRNA-seq Tuxedo Modules
    • CutAdapt
    • Fastq Length Filter
    • FASTQC
    • TopHat
    • Cufflinks
    • Cuffmerge
    • Cuffmergetocompare
    • Cuffdiff
    • R Summary Report
  • miRNA-seq Count Based Modules
    • CutAdapt
    • Fastq Length Filter
    • FASTQC
    • STAR Aligner
    • HTSEQ
    • R Summary Report - DESEQ2
  • ChIP-seq Modules – HOMER
    • FASTQC
    • ChIP trim
    • Bowtie
    • Read Density -HOMER
    • Peak Detection - HOMER
    • Peak Annotation & Visualization - HOMER
    • Find Motifs - HOMER
  • ChIP-seq Modules – MACS
    • FASTQC
    • ChIP trim
    • Bowtie
    • MACS
  • Whole Genome and Whole Exome Sequencing Modules
    • FASTQC
    • BWA-MEM
    • PICARD Mark Duplicates
    • GATK Preprocessing
    • GATK Variant Discovery
    • GATK Variant Filtering
  • Whole Genome Sequencing (MUTECT)
    • FASTQC
    • BWA-MEM
    • MUTECT
  • All Available Modules
  • Version History
    • 1.1.3 (2014/08/22)
    • 1.1.2b (2014/08/05)
    • 1.1.0 (2014/07/09)
    • 1.0.16 (2014/07/01)
    • 1.0.15 (2014/06/20)
  • Copyright & License
    • Omics Pipe
 
omics_pipe
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Copyright & License¶

Omics Pipe¶

MIT License (MIT)

Copyright (c) 2013 Kathleen Marie Fisch

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the “Software”), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

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© Copyright 2014, Kathleen Fisch, Ph.D.. Last updated on Jan 28, 2015.

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