sbamin

@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,

sbamin

Bootstrap: docker
From: python:3.10.11
Stage: build

%environment
    export my_appimg="cytotable_0.0.1p2"

%labels
    Maintainer sbamin
    Image CytoTable

sbamin

## 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)

sbamin

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() {

sbamin

#!/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"}"

sbamin

#!/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}"}"

sbamin

#!/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

sbamin

#!/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"}

sbamin

## 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,

sbamin

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

• When definining conda environments, prefer using channel priority in order of

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.