First let’s download and unzip GATK from github. It is open source, hosted on github, and available under a BSD 3-clause license. GATK is a toolkit developed by the broad institute focused primarily on variant discovery and genotyping. # make symlink ln -s ~/workspace/bin/bwa-0.7.17/bwa ~/workspace/bin/bwa # change to the bin folder, download, and extract the source code cd ~/workspace/bin Lets go ahead and make a bin directory in ~/workspace to get started. In this tutorial we will install tools in ~/workspace/bin. To start we must choose a single directory for installing tools, typically in linux, user compiled tools are installed in /usr/local/bin however backups of the tools we will be using have already been installed there. Prepare for installationįor this workshop we will be using the workspace folder to store results, executables, and input files. The remainder of this section will assume that you are on the AWS instance, however these instructions should work on any xenial ubuntu distribution with the required dependencies. However if you are interested in the underlying dependencies and how they were installed see the AWS AMI Setup page. If you are using the AWS instance built for this course these dependencies have already been installed. Note that depending on the operating system and environment, some additional dependencies would likely be needed. The instructions for installing these tools exist here. This workshop requires a large number of different bioinformatics tools.
0 kommentar(er)
