stevekm

Moved to https://github.com/JoshuaEstes/CheatSheets

stevekm

[source]

SSH login without password

Your aim

You want to use Linux and OpenSSH to automate your tasks. Therefore you need an automatic login from host A / user a to Host B / user b. You don't want to enter any passwords, because you want to call ssh from a within a shell script.

How to do it

First log in on A as user a and generate a pair of authentication keys. Do not enter a passphrase:

stevekm

#!/usr/bin/env python3

# do an action in parallel across multiple threads in Python
# example: get the average of lists of numbers

# references;
# https://stackoverflow.com/questions/8533318/multiprocessing-pool-when-to-use-apply-apply-async-or-map
# https://e2eml.school/multiprocessing.html
# https://docs.python.org/3.7/library/multiprocessing.html#multiprocessing.pool.Pool.apply_async

stevekm

You can use IGV to automatically & programmatically load genomic datasets and take snapshots of regions of interest. This is very handy and helps you avoid taking many screenshots manually.

Manual page here:

http://software.broadinstitute.org/software/igv/batch

These commands are also available:

http://software.broadinstitute.org/software/igv/PortCommands

stevekm

# ssh config to use with VS Code Remote SSH
# to launch a VS Code remote ssh session inside of 
# a new SLURM compute job running on the remote HPC

# when you start a new ssh session from your LOCAL laptop,
# SLURM will spin up a new srun job and connect to the ssh daemon on the compute node
# your ssh connection will thus tunnel from your LOCAL laptop
# through the head node, to the compute node
# the SLURM job on the compute node will remain active until it expires via time limit
# the SLURM job will terminate when the ssh session is closed

stevekm

Sophos

with Tamper Protection on you cannot normally remove the software, and a password is needed to disable Tamper Protection. However you can also disable it this way

with Tamper protection enabled

/Library/Application Support/Sophos/opm/Installer.app/Contents$ sudo ./MacOS/tools/InstallationDeployer --remove
Password:
Tamper protection check failed. Exiting.

stevekm

parallel -k -N0 -n 0 -j 4 "echo your command here ; sleep 2" ::: {1..10}

stevekm

apt-get install -y singularity-container=4.1.1+ds2-1ubuntu0.2

stevekm

[source]

This manual page is for Mac OS X version 10.9

If you are running a different version of Mac OS X, view the documentation locally:

    In Terminal, using the man(1) command

Reading manual pages

stevekm

#!/bin/bash

# on OS X, need to install ffmpeg
# so that we can convert FLAC music files
# into mp3 files

# install ffmpeg
brew install ffmpeg --with-fdk-aac --with-ffplay --with-freetype --with-libass --with-libquvi --with-libvorbis --with-libvpx --with-opus --with-x265
brew update && brew upgrade ffmpeg