RNAseq software installation on qbert or Simcenter clusters

====================For hisat2 and supporting programs
Install hisat2
ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.5-Linux_x86_64.zip

Install stringtie 1.3.1c
http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.3.1c.Linux_x86_64.tar.gz

Install samtools
https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
The above link is from http://www.htslib.org/download/
See also https://github.com/samtools/samtools/releases/


====================For R packages
Under shell, run R

Inside of R:
 source("https://bioconductor.org/biocLite.R")
 biocLite('ballgown')

 install.packages('devtools') #A USA mirror site may be chosen

 library(devtools)
 devtools::install_github('alyssafrazee/RSkittleBrewer') 

========== Testing the installation
Download the test files and codes from
ftp://ftp.ccb.jhu.edu/pub/RNAseq_protocol/

under shell
$ ./rnaseq_pipeline.config.sh
$./rnaseq_pipeline.sh out

=========Additional R packages
#Please also run the following code to install all packages in R. This may take 10-12 hours.
install.packages(new.packages())

#A prompt will ask for a mirror site. Any site from USA should work.