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