/tag/python
Future of Research Computing’s Training Initiatives: Workshops Survey
Please fill out the survey below to help us shape the future of Research Computing’s training initiatives: Link to Survey
Workshops
UVA Research Computing provides training opportunities covering a variety of data analysis, basic programming and computational topics. All of the classes listed below are taught by experts and are freely available to UVa faculty, staff and students.
New to High-Performance Computing? We have core training that is essential to getting up to speed working in the UVA HPC environment. We offer virtual orientation sessions to introduce you to the Afton & Rivanna HPC systems. Trainings are hosted Wednesdays. Registration is required.
The training material is hosted on our learning page where you can find a full YouTube video series and the workshop content of our core training.
education,
workshops
bioinformatics,
containers,
HPC,
image processing,
Ivy,
Matlab,
programming,
Python,
R,
Rivanna,
Shiny
Migrating Python packages
Scenario You have installed Python packages locally in one version and now wish to use them in a different version. For example, you have been using Python 3.6 but it is obsolete and will be removed soon, so you need to set up those packages for Python 3.8. There are several ways to accomplish this, depending on the package manager. In this how-to we will discuss pip and conda.
You will need to load the module for the newer Python version. For this example,
module load miniforge Pip The Python packages are installed in a hidden location under your home directory:
Refgenie: A Reference Genome Resource Manager
Reference genome assemblies are essential for high-throughput sequencing analysis projects. Typically, genome assemblies are stored on disk alongside related resources; e.g., many sequence aligners require the assembly to be indexed. The resulting indexes are broadly applicable for downstream analysis, so it makes sense to share them. However, there is no simple tool to do this.
Refgenie is a reference genome assembly asset manager. Refgenie makes it easier to organize, retrieve, and share genome analysis resources. In addition to genome indexes, refgenie can manage any files related to reference genomes, including sequences and annotation files. Refgenie includes a command line interface and a server application that provides a RESTful API, so it is useful for both tool development and analysis.
