We’ve installed software on the image, RNASeq_1DayWorkshop so you don’t have to waste time with installation during the workshop. If you would like to install this same set of software on your own hpcc or on another machine, some of these steps may work. We have tested and know the software works on an Ubuntu 18.04 base installation machine. We cannot guarantee that these lessons will work on other operating systems. (Based on Instructions from DIBSI)
Launch instance: “Ubuntu 18.04 Devel and Docker” base image (Oct 1, 2018 by jfischer), m1.large (CPU: 10, Mem: 30 GB, Disk: 60 GB)
Allocation Source: TG-MCG180142
Install in /opt, per Jetstream installation instructions:
sudo chmod a+w /opt
mkdir /opt/rnaseq
Download and install miniconda:
cd /opt/rnaseq
curl -O -L https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh #install in /opt/miniconda3
echo export PATH=$PATH:/opt/miniconda3/bin >> ~/.bashrc
source ~/.bashrc
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda
Install R Studio:
sudo apt-get update && sudo apt-get -y install gdebi-core r-base
Then:
wget https://download2.rstudio.org/rstudio-server-1.1.453-amd64.deb
sudo gdebi -n rstudio-server-1.1.453-amd64.deb
Trimmomatic and other software:
source ~/.bashrc
conda install -y fastqc multiqc trimmomatic trinity time osfclient salmon khmer
sudo apt-get install tree sl