Terminal application

The Research Environment runs on Linux. You can access the Terminal by clicking on the application on the Research Environment Desktop. From here you can access the file system and the HPC.

We do not allow you to use directory traversing to find genome files for participants, as you may find genomes of participants who have since withdrawn consent and any requests to export these data via Airlock will be rejected. The best way to find the locations of genome files is using the latest LabKey genome_file_types_and_paths table or file locations on the latest version Participant Explorer, as we know that these files are currently consented for use.

Resources for learning Bash

There are a variety of online resources for learning Bash and Bash scripting:

• The Linux Journey provides resources for learning about linux in general, which includes a section on working in the Shell and other sections on working with text (including stdin and stdout) and text editors and regular expressions.
• Ryans Tutorials has a comprehensive tutorial that covers all aspects of Bash and a short introduction to Linux and Bash scripting. It also has a command-line cheatsheet and Vim cheatsheet that might prove useful.
• For more in-depth Bash scripting, Ryans Tutorials also has a Bash scripting tutorial.
• IBM developerWorks has a 'Learn Bash By Example' section among some other in-depth Linux tutorials, it is split into three parts: Part 1 | Part 2 | Part 3.