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/