Adding custom file types in Pulsar IDE
Unrecognized file types are treated as plain text in Pulsar. I followed these steps to add a custom file type, so syntax highlighting etc. works.
Building PDF output in a Sphinx project using LaTeX on Linux
I’m doing this on Linux Mint 20.2, but these steps would also work on Ubuntu 20.04 LTS or derivatives.
My note-taking setup
An overview of my current note-taking set up using QOwnNotes and Nextcloud. I also discuss programs I have used in the past like Zim, org-mode and Joplin.
Convert Markdown to HTML using a custom Pandoc template
A tutorial on using Pandoc to convert Markdown to HTML using a CSS stylesheet and a custom template.
LaTeX
Underlines \underline{Text} A better approach https://alexwlchan.net/2017/10/latex-underlines/ Footnotes Within text, add a reference to the footnote item RiboPlot \ref{itm:riboplot} Then, add item to the footnote list at the end of the document...
List of useful software
Linux powerline-go A powerline style prompt written in Go.
KDE Plasma
Enable compose key in system settings This is useful when typing special characters like currency and typographic symbols like en dash, em dash etc., Open System Settings → Input Devices → Keyboard Click the Advanced tab (see screenshot below)...
VueJS
Install Vue cli using Yarn: cd Programs yarn add @vue/cli Added Programs/node_modules/.bin/vue to PATH Create project: vue create vue-weather
Markdown
Abbreviations Requires the Abbreviations extension. Include the expansion below the abbreviation. Using GPG as an example: *[GPG]: GNU Privacy Guard Images Syntax:  With links Include syntax for image where link...
Introducing Python programming to a general audience
This was my attempt at introducing Python to a general audience at Tech me out at home — an online event organised by Pint of Science, Ireland.
Web development
Insomnia REST client Installation on Ubuntu CSS Line numbers for code samples https://codepen.io/elomatreb/pen/hbgxp
def print_hi(name) puts "Hi, #{name}" end ...
Apt package manager
Apt is a package manager for Debian based distributions. Skip downloading translations To save bandwidth by not downloading package descriptions in languages other than English: echo 'Acquire::Languages "none";' | sudo tee...
Audacity
Improve Quality of Recorded Audio Reference: How To Improve Voice Quality in Audacity 2020 by CasualSavage on YouTube Wind noise can be reduced using a High Pass filter https://www.youtube.com/watch?v=5TZM6Wu6tiw Steps Remove noise Normalize...
AWS
Using s3cmd Reference Create a bucket aws s3 mb
Cockpit
Installation on Raspberry Pi 3 (Debian Stretch): echo 'deb http://deb.debian.org/debian stretch-backports main' > /etc/apt/sources.list.d/backports.list apt-get update apt-get install cockpit
Docker
Applying multiple tags to an image Reference You can apply the latest tag to a newly built image and add another tag that references a specific version. For example, to tag an image both as whenry/fedora-jboss:latest and whenry/fedora-jboss:v2.1,...
Emacs
Comment or Uncomment line: C-x C-;
Golang
Install Golang on Ubuntu sudo apt install golang-go Set GOPATH Add to .bashrc: export GOPATH=~/.go Source .bashrc or open a new terminal window. Install Programs Shiori Bookmark Manager https://github.com/go-shiori/shiori go get -u -v...
KVM
Ubuntu 18.04 on Wayland has no screen tearing issues. Noticed problems with xorg when maximising windows and performance was slow Steps to share folder with guest Reference Not working with CentOS 7 guest as there is no support for the 9p...
Logical Volume Management
Increasing storage space Note: These steps performed in a VirtualBox VM Shutdown VM, if it is running. From VirtualBox GUI, select VM -> Settings -> Storage. Select Controller: SATA -> click on the Adds hard disk button next to it. Select Create...
Lynis
Lynis is a security auditing tool for Linux Repository: https://github.com/CISOfy/lynis Installation Ubuntu 20.04 LTS The Lynis package is available in the repositories and can be installed using apt: sudo apt install lynis Ubuntu 18.04 LTS...
NodeJS
Installing NodeJS v14 and Yarn package manager on Ubuntu
Pygments
Pygments is a syntax highlighter for source code written in Python. An online demo is available. Generate default stylesheet pygmentize -S default -f html -a .highlight > default.css Generate SVG of source code pygmentize -f svg -l bash -O...
Spectre
A CSS framework Installation Create a directory for the project: mkdir project && cd project Initialise project: npm init Use npm to install spectre: npm install spectre.css --save Links Compiling custom version
BioVM 18.04.1
Summary of changes in BioVM 18.04.1 — a Linux virtual machine based on Ubuntu for teaching and learning Bioinformatics.
Android
Disable or Enable packages using adb Reference Connect device using USB or WiFi. List installed packages: adb shell pm list packages Find the name of package to disable — usually of the form com.developer.appname. To disable package: adb shell pm...
Flutter
Resources Build Native Mobile Apps with Flutter (Udacity) GitHub repository Disable analytics flutter config --no-analytics Change channel flutter channel beta flutter upgrade Build and release Reference Launcher icons Created a 192x192 SVG image...
Git
Create a zip archive of repository Reference git archive --prefix=riboplot/ -o /tmp/riboplot_0.3.1.zip HEAD Undo changes Reference When changes have already been pushed to a remote, use git revert: git revert commit_id Otherwise, to undo the last...
Learn Python With Me
An online Python course for beginners in programming
JavaScript
I prefer to install Node packages in a local directory ~/Programs/node_modules rather than using the global (-g) option which installs packages system wide which I’m not too comfortable with. Yarn Package Manager To initialise a repository to use...
Python GTK+ 3
Tutorial Scale image automatically to fit parent widget Reference allocation = parent_widget.get_allocation() desired_width = allocation.width desired_height = allocation.height pixbuf = gtk.gdk.pixbuf_new_from_file('your_image.png') pixbuf =...
Sphinx
Creating a Zeal docset from Sphinx documentation Using the pysam project documentation as an example. Create a directory for project: mkdir ~/Workspace/zeal/pysam cd ~/Workspace/zeal/pysam Create virtualenv, install latest release of pysam and...
Programming
General programming notes. Adding documentation to Devhelp Adding PyGobject docs as an example: git clone https://github.com/pygobject/pgi-docs-devhelp.git ~/.local/share/devhelp/books To update docs: cd ~/.local/share/devhelp/books git pull
PySide 2
Documentation https://wiki.qt.io/Qt_for_Python Tutorial: Data Visualization Tool Installation To create a virtual environment for PySide 2 projects: cd ~/.virtualenvs python3 -m venv pyside source pyside/bin/activate pip install --upgrade pip...
Video
Programs to Create Screencasts Record Desktop OBS Studio Simple Screen Recorder Record Terminal Sessions Asciinema Notes on Editing With Blender Output Format Dimensions HDTV 1080P or HDTV 720P Output File Format: FFmpeg video Container: MPEG-4...
Get lineage of an organism from NCBI taxonomy data
A Python script to obtain the complete taxonomic lineage of an organism from NCBI taxonomy data.
BioVM 18.04
A new release of BioVM with updated software, Galaxy configuration, documentation and includes recommendations for installing new software.
Conda
Install Miniconda 3 on Linux Download the latest version of the Miniconda installer (Python 3) from https://docs.conda.io/en/latest/miniconda.html Verify Download sha256sum Miniconda3-latest-Linux-x86_64.sh Ensure output matches the SHA256 is...
Running Galaxy project on Ubuntu 16.04 LTS
This is a step-by-step tutorial on running an instance of the Galaxy platform (v17.09) for biomedical research on Ubuntu 16.04 LTS.
Docker images for Bioinformatics software
How to run containers of VIGA, QIIME, PyFBA, Cutadapt and DADA2 and a helpful wrapper script for non-root users.
An unofficial VirtualBox image for QIIME 1
This is a VirtualBox VM I made for QIIME 1.9 based on the current version Ubuntu MATE LTS (16.04.3) with some additional improvements.
A Python script to update NCBI BLAST databases
Updating BLAST databases can can be done using the update_blastdb command but this script only updates databases if they are not being used.
Mercurial
From the perspective of a Git user Initialize a repository and create a default branch: hg init Status of a repository: hg status Meaning of the symbols displayed: ? file untracked. A file added for tracking/commit. M file modified. ! file...
Creating an online course using free and open source software
This post is about the free and open source software I used for creating an online course.