github config
1 min read Murray Cadzow
From August, github removed the use of authentication for https when using git.
If you had cloned repositories using https rather than ssh you will have issues with pulling and pushing to github.
For documentation about how to change to using ssh to …
Conda environments
3 min read Murray Cadzow
Using Conda on the server # Make conda available # latest version installed at time of post module load miniconda/Miniconda3_4.8.3 Conda environments Conda is a package manager that can make running software that requires specific versions of …
Adding Annotations to VCFs
2 min read Murray Cadzow
The main consideration is to make sure that the reference resource matches the genomic build of your VCF. i.e. make sure you are using GRCh37 resources for a GRCh37 aligned VCF, or GRCh38 resources for a GRCh38 aligned VCF.
dbSNP A vcf from dbSNP can …
Filtering VCF Annotations
4 min read Murray Cadzow
example.vcf.gz is a VCF file of three human subjects aligned to GRCh37 and varaint called following the GATK best practices that had been annotated with rsIDs from dbSNP v151 and further annotated using dbNSFP4.0a and snpEff so includes annotations …
More on less
3 min read Riku Takei
This post will cover some of the useful features in less that will let you look at any text-based document like a wizard!!
Scroll through page-wise As you may already know, you can use <space> to move one window forward in the document, but did …
GNU parallel
4 min read Riku Takei
Intro GNU parallel (commonly referred to as just parallel) is a command line tool that allows you to run multiple independent tasks at the same time by using the available cores on a computer.
This post will cover:
How to use parallel Some useful …
Beyond Software Carpentry Git
5 min read Riku Takei
Intro Once you have finished Software Carpentry Git lesson, you should be able to do basic version controlling with Git. You would have learnt how to:
Stage and commit your changes Make a remote GitHub repository Push and pull from your remote …
A beginner's guide to making new posts with Hugo
3 min read Riku Takei
What is Hugo? Hugo is a popular static site generator written in Go language. It’s static in the sense that the web pages do not change depending on who visits the site (for example, contents do not change for different user) – all the …