This is part II of the workshop which prepares a biologist to work in an interactive Linux environment of our BioHPC Lab workstations. It will show how to transfer data between the workstations and the outside world, how to run the next-gen data analysis programs and construct simple pipelines using rudimentary scripting techniques. Please note: running of the data analysis applications will be presented from the operating system point of view - please read the lecture slides from the workshop Using BioHPC Lab Software, BioHPC Laboratory to learn more about the biological context of these programs.
This part of the workshop will cover the following topics:
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Reminder: Overview of computational infrastructure at CBSU
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Transferring files to and from BioHPC Lab workstations
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Basic operations on files
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Running command line programs on BioHPC Lab workstations
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Basics shell and perl scripting
The presented material will be illustrated by hands-on exercises hosted on dedicated workstations of the CBSU BioHPC Lab. The workstations will be accessed using the Secure SHell (ssh) protocol. To participate in the exercises, please bring your own laptop with an ssh client installed. MACs and Linux laptops come with native ssh clients and no extra installtion is needed. For windows, the recommended ssh client is PuTTy - please install it prior to the workshop. To be able to run Linux programs with graphical inerface displaying on your Windows laptop, you should also install Xming (this is not essential for the workshop). To transfer files between your laptop and a Linux machine, you will need an sftp clinet, such as FileZilla on Windows (MAC and Linux laptops come with native sfpt clients and no extra installation is needed). For links to client software mentioned above, instructions, and more information on access to BioHPC machines, please refer to the following document: http://cbsu.tc.cornell.edu/lab/doc/Remote_access.pdf, especially points 1 and 2.2-2.4.
Access to BioHPC Lab workstations requires a Lab account. If you do not yet have an account on BioHPC Lab system, we will create one for you. Also, we will assign a machine for you to work on during and after the workshop. The machine allocations will be posted on this page. Machine reservations will be active from Mon March 11th 3:00PM to end of the day Wed March 13th.
machine allocations
Lecture slides