UCSC Genome Browser – Docker solution for a self -hosted instance

The idea of being able to browse a genome using a great solution such as the UCSC Genome Browser seemed really interesting to me. Fortunately, using Docker it is possible with a few steps. We will need two docker containers. One for Apache and another for the database - MySQL. The Apache container will retrieve … Continue reading UCSC Genome Browser – Docker solution for a self -hosted instance

Environment Modules – Dynamic environment using modulefiles

The main idea of Environment Modules is to help you manipulate the environment loading and unloading modules. Environment Modules is a powerful tool with many options. Here we just give it a try. Using a Fedora:31 docker image lets play : docker run -ti fedora:31 bash Now lets install Environment modules: dnf update -y dnf … Continue reading Environment Modules – Dynamic environment using modulefiles

European Nucleotide Archive (ENA) and REST – retrieving NGS data links.

From time to time I get a list of ids such as: ERR3277096 ERR3277097 ERR3277098 ERR3277099 along with a request for analysis of the data. Those ids are the so called "Run accession" ids. They usually point out to NGS data that have been deposited in public databases such as SRA, ENA and others. I … Continue reading European Nucleotide Archive (ENA) and REST – retrieving NGS data links.

Github – Atom feed for releases

If you don't want to check Github pages to get to know when new releases are coming, there is a neat and easy solution for that. Github provides a atom address that allows you to get informations about new releases. The pattern is: https://github.com/user/repository/releases.atom I use Newsboat to check RSS feeds. Into .newsboat directory, the … Continue reading Github – Atom feed for releases

GNU Make – Install and maintain multiple tools and versions

The idea is to use the power of GNU Make to simplify installing and maintaining multiple tools with multiple versions. The point on keeping multiple versions is to be able to: 1 - Reproduce results from papers; 2 - Be able to reproduce your own results from the past. The way I organize it is … Continue reading GNU Make – Install and maintain multiple tools and versions

setfacl – Setting file Access Control Lists (ACLs)

According to Wikipedia ACLs: "...is a list of permissions attached to an object." "An ACL specifies which users or system processes are granted access to objects, as well as what operations are allowed on given objects." meaning that ACL is an "alternative" to the traditional unix permission system. Now, to the CLI! Setfacl help provides: … Continue reading setfacl – Setting file Access Control Lists (ACLs)