Posts Tagged ‘config’

bowtie2: Relaxed Parameters for Generous Alignments to Metagenomes

   Sam Nicholls    No Comments yet    Tools

Even `bowtie2`’s `–very-sensitive-local` option can be a little grumpy. Here’s how I make `bowtie2` a little more relaxed for alignment of more dissimilar sequences, particularly for my work on metagenomes.


An idiot’s guide to Python documentation with Sphinx and ReadTheDocs

   Sam Nicholls    No Comments yet    Documentation, Python

This is the third occasion that I’ve come to set up a Python package’s documentation. It is also the third occasion where I’ve spent many hours and commits trying to work out how I made everything work last time. So for my future sanity and possibly yours, here’s a quick guide on setting up Sphinx-based, ReadTheDocs-hosted Python documentation.


Using fail2ban to mitigate simple DOS attacks against apache (or why I am a terrible sysop)

   Sam Nicholls    No Comments yet    Devops, System Administration

Earlier this afternoon, my server was upset. Here’s what happened, how it took so long to find out, and how I will try and stop it happening again. In particular, I provide configuration for a `fail2ban` jail to try and stop simple DOS, that actually works.