tomkinsc

#!/bin/bash

# Disable web URL link previews in Apple Mail under macOS 13.x Ventura (14.x+ has a UI setting to do so).
#   from:
#   https://apple.stackexchange.com/questions/450339/turn-off-link-preview-in-mail#comment669426_457934

sudo defaults write /Library/Preferences/FeatureFlags/Domain/Mail.plist RichLinks -dict-add Enabled -bool NO
sudo chmod -R o+rX /Library/Preferences/FeatureFlags

tomkinsc

#!/bin/bash

sudo powermetrics --samplers smc |grep -i "CPU die temperature"
# or thermal pressure:
# sudo powermetrics -s thermal | grep "Current pressure"

# ...or just install the "Hot" menubar app:
# https://github.com/macmade/Hot

tomkinsc

#!/bin/bash

if [ $# -eq 0 ]; then
    echo "This script can be used to transfer all files from a BaseSpace project "
    echo "Usage: $0 BaseSpaceProjectName DNAnexusProjectName"
    echo "       Before running, be sure to log in to BaseSpace"
    echo "          bs auth"
    echo "       The CLI toolkits for bs and dx can be found here and must be installed first:"
    echo "          https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview"
    exit 1

tomkinsc

#!/bin/bash

if [ $# -eq 0 ]; then
    echo "This script can be used to transfer all files from a DNAnexus project to a GS bucket for Terra."
    echo "Usage: $0 DNAnexus_project-id:/path/to/recurse gs://bucket/path [pattern_to_match]"
    echo "       Before running, be sure to log in to both BaseSpace and DNAnexus via:"
    echo "          dx login"
    echo "       The CLI toolkits for bs and dx can be found here and must be installed first:"
    echo "          https://documentation.dnanexus.com/downloads"
    exit 1

tomkinsc

#!/bin/bash

# First get auth token: https://api.firecloud.org/#/Profile/getProxyGroup

# Check to see if a pipe exists on stdin.
if [ -p /dev/stdin ]; then
        while IFS= read emailaddress; do
                printf "$emailaddress\t"
                curl -X 'GET' \
                  "https://api.firecloud.org/api/proxyGroup/$(echo $emailaddress | sed 's/@/%40/')" \

tomkinsc

wget -q https://packages.microsoft.com/config/ubuntu/$(lsb_release -rs)/packages-microsoft-prod.deb
sudo dpkg -i packages-microsoft-prod.deb
rm packages-microsoft-prod.deb
sudo apt-get update
sudo apt-get install powershell
hash -r

pwsh
Install-Module -Name PSWSMan

tomkinsc

Native VPN killswitch for macOS

This creates a daemon job to watch VPN and Wi-Fi state to ensure the native macOS VPN is active if it drops and is no longer active, or if there is a change in Wi-Fi state (as in the case of Wi-Fi being turned on).

Install instructions

• customize the string variables at the top of vpn-killswitch.sh to the name of your Wi-Fi network and VPN configuration
• Place the vpn-killswitch.sh file somewhere, make it executable (chmod u+x vpn-killswitch.sh)
• alter the full path to whereever the script was placed in the on-network-change.job.plist file
• (Change the line with /Users/MYUSERNAME/full/path/to/vpn-killswitch.sh)

tomkinsc

#!/usr/bin/env python

import re, sys, os
from stat import S_ISFIFO
import argparse

# quick and dirty script to show emoji or bars for samtools mpileup quality scrores
# extra verbose so this does not require any external libraries
# based on fastqe and emojify:
    # https://raw.githubusercontent.com/fastqe/fastqe/master/fastqe/fastqe_map.py

tomkinsc

||id.google.com^
||accounts.google.com/gsi/$3p

tomkinsc

#!/usr/bin/env python

import sys, re

flowcell_to_machine_model_and_chemistry = {
    r'[A-Z,0-9]{5}AAXX':{
        "machine":    "Illumina Genome Analyzer IIx",
        "chemistry":  "All",
        "lane_count":  8,
        "note":       ""