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 And you may need to make adjustments if it is out of date.
What do these scripts do?¶
Cleans up the existing environment - Removes
These older files are removed.
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)
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