quick-install.md

Quick install scripts

bash/ contains simple bash scripts to automate some of the installation of riboviz's dependencies. They are the manual commands of Install riboviz and dependencies in bash script form.

These scripts were written for Ubuntu 18.04 and CentOS 7.4.

Running these scripts requires you to have permission to run sudo to install and configure software. If you don't have sudo access you will have to ask a local system administrator to run these commands for you.

Note: These scripts are not robust and do not perform any error handling.

Authenticate with sudo:

$ sudo su -
CTRL-D

Install operating system packages and R:

• Ubuntu:

$ source bash/install-ubuntu.sh

• CentOS:

$ source bash/install-centos.sh

Install R packages:

$ Rscript rscripts/install_r.R

Check that R's library paths include your personal library:

$ Rscript -e ".libPaths()"

You should see something like:

• Ubuntu:

[1] "/home/ubuntu/R/x86_64-pc-linux-gnu-library/3.4"
[2] "/usr/local/lib/R/site-library"                 
[3] "/usr/lib/R/site-library"                       
[4] "/usr/lib/R/library"     

• CentOS:

[1] "/home/centos/R/x86_64-redhat-linux-gnu-library/3.5"
[2] "/usr/lib64/R/library"                              
[3] "/usr/share/R/library"  

Install Miniconda Python 3 and Python packages:

$ source bash/install-py.sh

Install Hisat2 and Bowtie:

$ source bash/install-tools.sh

Create set-riboviz-env.sh:

$ source bash/create-set-riboviz-env.sh