Samir Amin sbamin

Tips from Johannes Köster - Author of Snakemake on advanced use of snakemake

bioconda > conda-forge > anything else

When definining dependencies for conda env, never ever use version constraints beyond major.minor(1.2) or rarely use major.minor.patch(1.2.3)
You should never use full version major.minor.patch-blah_blah like libgcc-ng=7.2.0=hdf63c60_3. Specifying full versions will inevitably fail future snakemake runs as conda website can not maintains all work-in-progress (like major.minor.patch-blah_blah) on its website.


	@ARTICLE{Bakas2020-ee,
	title = "{iGLASS}: imaging integration into the Glioma Longitudinal
	Analysis Consortium",
	author = "Bakas, Spyridon and Ormond, David Ryan and Alfaro-Munoz, Kristin
	D and Smits, Marion and Cooper, Lee Alex Donald and Verhaak, Roel
	and Poisson, Laila M",
	journal = "Neuro. Oncol.",
	volume = 22,
	number = 10,

	## add following to mac ~/.ssh/config file after required edits
	## then do ssh mcclearybg to start background session, typically
	## once per day. This will require duo push
	## then you can start additional ssh by ssh mccleary (note: no suffix bg)

	## More at https://docs.ycrc.yale.edu/clusters-at-yale/access/advanced-config/ and
	## https://www.anchor.com.au/blog/2010/02/ssh-controlmaster-the-good-the-bad-the-ugly/

	################## Yale ##################
	# Uncomment the ForwardX11 options line to enable X11 Forwarding by default (no -Y necessary)

	javascript:(function(){
	// via ChatGPT, https://shareg.pt/dIVonZZ
	var highlights = [];
	var style = document.createElement("style");
	style.type = "text/css";
	style.innerHTML = ".highlight { background-color: yellow !important; color: black !important; }";

	document.getElementsByTagName("head")[0].appendChild(style);

	document.addEventListener("mouseup", function() {

	#!/usr/bin/env bash

	## Enable/Disable sleep on closed display

	## strict mode on
	set -euo pipefail

	## can be one of status\|on\|off
	cmd="${1:-"status"}"

	#!/usr/bin/env bash

	## Check CPU and Memory Usage for an USER
	## @sbamin
	## https://superuser.com/a/920158/213756

	## default to current user unless an user is specified as
	## a first positional argument.
	userid="${1:-"${USER}"}"

	#!/usr/bin/env bash

	# wrapper for running deno (dependency for Quarto) on Cent OS 7
	# https://github.com/quarto-dev/quarto-cli/discussions/380

	# this wrapper replaces default deno binary (at /share/deno)
	# shipped with quarto pre-compiled binaries
	# tested ok with https://github.com/quarto-dev/quarto-cli/releases/download/v0.9.254/quarto-0.9.254-linux-amd64.tar.gz
	# on Cent OS 7, Linux 3.10.0-1062.1.2.el7.x86_64

	#!/usr/bin/env bash

	## following will prevent running of queued jobs if tier 1 space is > 99 %
	tstamp="$(date +%d%b%y_%H%M%S_%Z)"

	## available files: tier1state.txt, tier2state.txt, faststate.txt
	## These files updates every 30 min per disk status.
	diskstat=$(cat /projects/verhaak-lab/verhaak_env/SetEnv/logs/diskstats/tier1state.txt)
	diskstat=${diskstat:-"NA"}

	## add following to the end of ~/.bash_profile assuming ~/.bash_profile takes the precedence over ~/.profile (if present), ~/.bash_profile, or other bash configs.
	## for zsh or other shells, you may need to tweak following code.
	## Be careful "resetting" PATH variable and know the implications of PATH variable being either empty or missing critical system paths!

	################################### SET PATH ###################################
	## User specific environment and startup programs
	## Rewriting PATH ##
	## We want user and anaconda paths to precede system paths, esp. this string:
	## /usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin which contains
	## most of system default libs,