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.

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"))

RNA-seq (Tuxedo)

FASTQC:	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
TOPHAT:	http://tophat.cbcb.umd.edu/
CUFFLINKS:	http://cufflinks.cbcb.umd.edu/

RNA-seq (Anders 2013)

FASTQC:	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
STAR:	http://code.google.com/p/rna-star/
SAMTOOLS:	http://samtools.sourceforge.net/
HTSEQ:	http://www-huber.embl.de/users/anders/HTSeq/doc/index.html

Whole Exome Sequencing (GATK)

FASTQC:	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
BWA:	http://bio-bwa.sourceforge.net/
PICARD:	http://picard.sourceforge.net/
GATK:	https://www.broadinstitute.org/gatk/download

Whole Genome Sequencing (GATK)

FASTQC:	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
BWA:	http://bio-bwa.sourceforge.net/
PICARD:	http://picard.sourceforge.net/
GATK:	https://www.broadinstitute.org/gatk/download

Whole Genome Sequencing (MUTECT)

FASTQC:	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
BWA:	http://bio-bwa.sourceforge.net/
MUTECT:	http://www.broadinstitute.org/cancer/cga/mutect

ChIP-seq (MACS)

FASTQC:	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
HOMER:	http://homer.salk.edu/homer/ngs/index.html
BOWTIE:	http://bowtie-bio.sourceforge.net/index.shtml
MACS:	http://liulab.dfci.harvard.edu/MACS/
BEDTOOLS:	https://github.com/arq5x/bedtools2
SAMTOOLS:	http://samtools.sourceforge.net/

ChIP-seq (HOMER)

FASTQC:	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
HOMER:	http://homer.salk.edu/homer/ngs/index.html
BOWTIE:	http://bowtie-bio.sourceforge.net/index.shtml
BEDTOOLS:	https://github.com/arq5x/bedtools2
SAMTOOLS:	http://samtools.sourceforge.net/

Breast Cancer Personalized Genomics Report- RNAseq

FASTQC:	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
STAR:	http://code.google.com/p/rna-star/
SAMTOOLS:	http://samtools.sourceforge.net/
HTSEQ:	http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
RSEQC:	http://rseqc.sourceforge.net/
PICARD:	http://picard.sourceforge.net/
GATK:	https://www.broadinstitute.org/gatk/download
FusionCatcher:	https://code.google.com/p/fusioncatcher/
Oncofuse:	http://www.unav.es/genetica/oncofuse.html
BWA:	http://bio-bwa.sourceforge.net/
DNANEXUS SAMTOOLS:	https://github.com/dnanexus/samtools
BEDTOOLS:	https://github.com/arq5x/bedtools2
BLAT:	https://genome.ucsc.edu/FAQ/FAQblat.html#blat3
SNPiR:	http://lilab.stanford.edu/SNPiR/
SNPEFF:	http://snpeff.sourceforge.net/
SNPSIFT:	http://snpeff.sourceforge.net/SnpSift.html
VCFTOOLS:	http://vcftools.sourceforge.net/

TCGA Reanalysis Pipeline - RNAseq

GeneTorrent:	https://cghub.ucsc.edu/docs/user/software.html
FASTQC:	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
STAR:	http://code.google.com/p/rna-star/
SAMTOOLS:	http://samtools.sourceforge.net/
HTSEQ:	http://www-huber.embl.de/users/anders/HTSeq/doc/index.html
RSEQC:	http://rseqc.sourceforge.net/
PICARD:	http://picard.sourceforge.net/
GATK:	https://www.broadinstitute.org/gatk/download
FusionCatcher:	https://code.google.com/p/fusioncatcher/
Oncofuse:	http://www.unav.es/genetica/oncofuse.html
BWA:	http://bio-bwa.sourceforge.net/
DNANEXUS SAMTOOLS:	https://github.com/dnanexus/samtools
BEDTOOLS:	https://github.com/arq5x/bedtools2
BLAT:	https://genome.ucsc.edu/FAQ/FAQblat.html#blat3
SNPiR:	http://lilab.stanford.edu/SNPiR/
SNPEFF:	http://snpeff.sourceforge.net/
SNPSIFT:	http://snpeff.sourceforge.net/SnpSift.html
VCFTOOLS:	http://vcftools.sourceforge.net/

TCGA Reanalysis Pipeline - RNAseq Counts

GeneTorrent:	https://cghub.ucsc.edu/docs/user/software.html
FASTQC:	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
STAR:	http://code.google.com/p/rna-star/
SAMTOOLS:	http://samtools.sourceforge.net/
HTSEQ:	http://www-huber.embl.de/users/anders/HTSeq/doc/index.html

miRNAseq Counts (Anders 2013)

CutAdapt:	http://code.google.com/p/cutadapt/
FASTQC:	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
STAR:	http://code.google.com/p/rna-star/
SAMTOOLS:	http://samtools.sourceforge.net/
HTSEQ:	http://www-huber.embl.de/users/anders/HTSeq/doc/index.html

miRNAseq (Tuxedo)

CutAdapt:	http://code.google.com/p/cutadapt/
FASTQC:	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
TOPHAT:	http://tophat.cbcb.umd.edu/
CUFFLINKS:	http://cufflinks.cbcb.umd.edu/