Jacques Dainat Juke34

Create Dockerfile

Create a file called anvio_dockerfile and copy paste the following in it and save:

FROM condaforge/miniforge3:24.7.1-2

RUN conda create -y --name anvio-dev python=3.10

RUN conda install -y -c conda-forge -c bioconda python=3.10 \

How to install GUIX on M2 Mac computer

Downloading & installing UTM

You need to install the UTM virtual machine manager In your browser, go to mac.getutm.app, and click on the Download button.

Mount the downloaded UTM.dmg disk-image and drag the UTM app to the Applications folder. Next, launch the UTM app from your Mac’s local Applications folder. (Depending on your Mac’s security settings, you may get a confirmation dialog when you launch UTM for the first time. If such a dialog appears, choose Open.)

Making a good genome annotation using MAKER3

Foreword

Making a good annotation isn't easy, MAKER or not MAKER!
Here I explain the main steps to avoid the pitfalls and make a good annotation using the MAKER annotation tool.

Information on commands and protocols can also be found here: https://nbisweden.github.io/workshop-genome_annotation_elixir/exercises

Two possibilities well known: https://github.com/ohmybash/oh-my-bash and https://github.com/nojhan/liquidprompt

Liquid prompt

clone the repo

cd ~
git clone https://github.com/nojhan/liquidprompt.git ~/liquidprompt

Tutorial: Greatly speed up conda by using mamba

From rpolicastro on https://www.biostars.org/p/9461665/

Conda has been my go-to software manager, but it was only recently brought to my attention that a well maintained project has aimed to greatly speed up and improve the conda functions. Mamba is an almost complete rewrite of conda in C++, allows for parallel downloading of data, and has faster (and better) dependency resolving. For working with larger environments I’ve noticed tasks that would take tens of minutes only takes minutes now (if not less).

Below I’ll provide a quick tutorial on working with mamba, which in theory mirrors what one would do with conda. You should have at least miniconda3 installed.

Installing Mamba

Your conda base environment is the environment where the conda software lives, and additionally any software in base gets added to your path. Generally you don’t want to install software into the base environment., however in this particular case you need to install mamba here,

	# Create local and remote repo from loca (name of the repo:my repo)
	mkdir myrepo # create folder that will hold my repo
	cd myrep # mv into the folder
	git init # initialize the folder as a git repo
	touch .gignore # create a file, here a gitignore file
	git add .gignore # add a file to be tracked by git
	git commit -m "add gignore" # commit the modif
	remote add myrep git@address_to_the_rep # Specify what will be the name of the remote repo and the address to this remote repo
	git push --set-upstream origin master # tell git to link the remote repo (origin) to the local master one.

	First copy this file: https://github.com/git/git/blob/master/contrib/completion/git-prompt.sh

	Then add in the bashrc the following lines:

	source /path/to/git-prompt.sh
	GIT_PS1_SHOWDIRTYSTATE=true
	GIT_PS1_SHOWUNTRACKEDFILES=true
	GIT_PS1_SHOWSTASHSTATE=true
	GIT_PS1_SHOWUPSTREAM="auto"
	GIT_PS1_SHOWCOLORHINTS=true

	# Migration
	https://www.mikestreety.co.uk/blog/migrating-gitlab-from-one-server-to-another/

	# Count column in a file
	awk '{print NF}' file \| sort -nu \| tail -n 1