=======================
Third Party Software Dependencies
=======================
Omics Pipe is dependent upon several third-party software packages. Before running Omics Pipe, please install all of the
required tools for the pipeline you will be running (see below) as `Modules`_ on your local cluster. If you are running the AWS
distribution, all third party software is already installed.
.. _Modules: http://modules.sourceforge.net/
.. rst-class:: html-toggle
R Packages Needed
===================
In R, you can cut and copy this to install all required packages::
install.packages(c("bibtex", "AnnotationDbi", "cluster", "cummeRbund", "data.table", "DBI", "DESeq2", "devtools", "dplyr", "gdata",
"ggplot2", "graphite", "igraph", "KEGGREST","knitr", "knitrBootstrap", "lattice", "locfit", "pamr", "pander", "pathview",
"plyr","RColorBrewer","Rcpp", "RcppArmadillo", "RCurl", "ReactomePA", "RefManageR","RJSONIO","RSQLite",
"stringr","survival", "XML", "xtable", "yaml"))
.. rst-class:: html-toggle
RNA-seq (Tuxedo)
===================
.. rst-class:: html-plain-table
====================== ===================================================
FASTQC: ``_
TOPHAT: ``_
CUFFLINKS: ``_
====================== ===================================================
.. rst-class:: html-toggle
RNA-seq (Anders 2013)
=======================
.. rst-class:: html-plain-table
====================== ===================================================
FASTQC: ``_
STAR: ``_
SAMTOOLS: ``_
HTSEQ: ``_
====================== ===================================================
.. rst-class:: html-toggle
Whole Exome Sequencing (GATK)
============================
.. rst-class:: html-plain-table
====================== ===================================================
FASTQC: ``_
BWA: ``_
PICARD: ``_
GATK: ``_
====================== ===================================================
.. rst-class:: html-toggle
Whole Genome Sequencing (GATK)
=================================
.. rst-class:: html-plain-table
====================== ===================================================
FASTQC: ``_
BWA: ``_
PICARD: ``_
GATK: ``_
====================== ===================================================
.. rst-class:: html-toggle
Whole Genome Sequencing (MUTECT)
=================================
.. rst-class:: html-plain-table
====================== ===================================================
FASTQC: ``_
BWA: ``_
MUTECT: http://www.broadinstitute.org/cancer/cga/mutect
====================== ===================================================
.. rst-class:: html-toggle
ChIP-seq (MACS)
======================
.. rst-class:: html-plain-table
====================== ===================================================
FASTQC: ``_
HOMER: ``_
BOWTIE: ``_
MACS: ``_
BEDTOOLS: ``_
SAMTOOLS: ``_
====================== ===================================================
.. rst-class:: html-toggle
ChIP-seq (HOMER)
====================
.. rst-class:: html-plain-table
====================== ===================================================
FASTQC: ``_
HOMER: ``_
BOWTIE: ``_
BEDTOOLS: ``_
SAMTOOLS: ``_
====================== ===================================================
.. rst-class:: html-toggle
Breast Cancer Personalized Genomics Report- RNAseq
================================
.. rst-class:: html-plain-table
====================== ===================================================
FASTQC: ``_
STAR: ``_
SAMTOOLS: ``_
HTSEQ: ``_
RSEQC: ``_
PICARD: ``_
GATK: ``_
FusionCatcher: ``_
Oncofuse: ``_
BWA: ``_
DNANEXUS SAMTOOLS: ``_
BEDTOOLS: ``_
BLAT: ``_
SNPiR: ``_
SNPEFF: ``_
SNPSIFT: ``_
VCFTOOLS: ``_
====================== ===================================================
.. rst-class:: html-toggle
TCGA Reanalysis Pipeline - RNAseq
=========================
.. rst-class:: html-plain-table
====================== ===================================================
GeneTorrent: ``_
FASTQC: ``_
STAR: ``_
SAMTOOLS: ``_
HTSEQ: ``_
RSEQC: ``_
PICARD: ``_
GATK: ``_
FusionCatcher: ``_
Oncofuse: ``_
BWA: ``_
DNANEXUS SAMTOOLS: ``_
BEDTOOLS: ``_
BLAT: ``_
SNPiR: ``_
SNPEFF: ``_
SNPSIFT: ``_
VCFTOOLS: ``_
====================== ===================================================
.. rst-class:: html-toggle
TCGA Reanalysis Pipeline - RNAseq Counts
=========================
.. rst-class:: html-plain-table
====================== ===================================================
GeneTorrent: ``_
FASTQC: ``_
STAR: ``_
SAMTOOLS: ``_
HTSEQ: ``_
====================== ===================================================
.. rst-class:: html-toggle
miRNAseq Counts (Anders 2013)
=========================
.. rst-class:: html-plain-table
====================== ===================================================
CutAdapt: ``_
FASTQC: ``_
STAR: ``_
SAMTOOLS: ``_
HTSEQ: ``_
====================== ===================================================
.. rst-class:: html-toggle
miRNAseq (Tuxedo)
=========================
.. rst-class:: html-plain-table
====================== ===================================================
CutAdapt: ``_
FASTQC: ``_
TOPHAT: ``_
CUFFLINKS: ``_
====================== ===================================================