Setting Up Quest

Setting up your environment

In order to do any sort of analysis you will need to set up your environment first. Daniel Cook has written a script that will set up the environment on quest. The script works as of 2017-12-05. However, because software gets updated frequently it may break and may need to be updated. However - it will get you 90% of the way there. You need to read the script before running it and to understand what it is doing. And you may need to make adjustments if it is out of date.

Quest Setup Scripts

What do these scripts do?

Cleans up the existing environment - Removes ~/.linuxbrew and ~/.cache

These older files are removed.

Installs linuxbrew

Linuxbrew is the tool used to install additional software.

Installs the following software

curl
git
nextflow
pigz
igvtools
vcfanno
snpeff
fastq-tools
muscle
sambamba
google-cloud-sdk
# utilities
pyenv
pyenv-virtualenv
autojump

Replaces your .bash_profile

The .bash_profile will be replaced with the one found on the Quest Setup Scripts page.

Installs Python 2.7.11 and Python 3.6.0

These are installed using pyenv.

python 2.7.11 is set as the default global version.

Installs python modules for python 2.7.11

pip
numpy
setuptools
cython
scipy
gcloud
vcf-kit
bam-toolbox (for coverage calculations)

Configures nextflow

See Quest-Nextflow for further details on what exactly is being done here.

... And More

Please read the script prior to running it.

Running the script

curl https://gist.github.com/danielecook/aed4a6fd53195fca7a3297f054d613c7#file-quest_setup-sh | bash