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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.)

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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

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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

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

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# 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.

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

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Google Search Operators blog: https://ahrefs.com/blog/google-advanced-search-operators/

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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

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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,

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How to sort a tuple

similar to the NF docu example for values

Channel
    .from( 1, 2, 3, 4, 5 )
    .filter { it % 2 == 1 }
    .view()

but addressing the tuple elements as required