NIH HPC News & Announcements
Upcoming classes taught by the NIH Helix/Biowulf staff
Date: 27 March 2017 12:03:16
From: Helix Systems Staff
The Helix/Biowulf staff will present two classes in April &
May 2017. These classes are hands-on and each will be
taught in a single 3 hour morning session.
Classes are free but registration is required. Helix/Biowulf
users will take priority when enrolling in the second class
on Snakemake.
These classes can be taken individually or as a pair. No
previous bioinformatics expertise is assumed or necessary.
Creating and running software containers with Singularity
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Date & Time: Monday 24 April, 9:00 am - 12:00 pm
Location: Bldg 10, NIH Library Training Room, First Floor
Containers give you the freedom to install custom software
in a portable virtual environment. This environment can be
copied and shared fostering collaboration and
reproducibility.
In this workshop, you will use Singularity to create and run
containers. You will learn how to install Singularity on
your Linux system, create containers with your choice of
Linux distribution and software, and use Singularity to run
containerized apps. As a concrete example, you will create a
container for reproducible bioinformatic workflows. When
finished this environment will include software such as
fastqc, STAR, RSeQC, picard, sailfish, featureCounts, and
several R packages. This container will be used in the
follow-up class on building a reproducible workflow with
Snakemake.
PLEASE NOTE: As a prerequisite, students MUST have access to
their own Linux environment with the ability to execute
commands as the root user. A Linux laptop, a virtual machine
(VM), or a cloud instance should fulfill this requirement.
A Helix/Biowulf account will NOT fulfill this requirement.
Ubuntu 14.04/16.04 or CentOS 6/7 are preferred for this
class. Laptops with ssh clients will be provided for users
to access their own cloud instances where applicable. If you
are unsure whether you have a Linux environment that meets
the requirements for this class please contact the
instructor (Dave Godlove) in advance for clarification or
advice (staff@helix.nih.gov).
Building a reproducible workflow with Snakemake and
Singularity
------------------------------------------------------------
Date & Time: Monday 01 May, 9:00 am - 12:00 pm
Location: Bldg 10, NIH Library Training Room, First Floor
Students attending this class will learn the basics of
building bioinformatics workflows with Snakemake and will
learn how to make them reproducible by combining Snakemake
with tools in a singularity container. During this class we
will develop the beginnings of a basic RNASeq pipeline for
gene-level differential expression analysis and will use the
example container built in the preceding Singularity class.
This class will make use of the Biowulf cluster and basic
knowledge of the Linux command line as well as python are
required.
Registration for all classes is available at
https://hpc.nih.gov/nih/classes/
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