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Mitchells shell tips

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Mitchell Robert Vollger edited this page Jan 3, 2023 · 7 revisions

.bashrc additions or shell configuration

For easy project sharing add this to your .bashrc 

umask 002

Using SMRTlink tools

PATH=$PATH:/gscratch/stergachislab/install_dir/smrtlink/smrtcmds/bin/

More detailed squeue results

 alias myq=$'squeue -u $(whoami) -o $\'%A\t%u\t%C\t%m\t%a\t%M\t%p\t%T\t%r\t%j\t%N\' --noconvert | column -t'

Better history with the up arrow in shell

For better history text completion in bash add the following to ~/.inputrc:

# Press up-arrow for previous matching command
"\e[A":history-search-backward
# Press down-arrow for next matching command
"\e[B":history-search-forward

see for details: https://unix.stackexchange.com/questions/96510/search-for-a-previous-command-with-the-same-prefix-when-i-press-up-at-a-shell-pr

bash scripting

Start every bash script with

These options make it so that once there is an error in the bash script the script ends with an error status. It also errors if there are unset variables (-u).

#!/usr/bin/env bash                                                                                                                                                                                            
set -euo pipefail

ssh tips

Want to only ssh in once per terminal, add this to a file called ~/.ssh/config to set up something called a controlmaster .

Host stergachis
  HostName klone.hyak.uw.edu    
  User mvollger
  controlmaster auto
  controlpath /tmp/ssh-ster-%r@h:%p
  ServerAliveInterval 60
  ForwardAgent yes

modify your user name, and then type:

ssh stergachis

and then all subsequent calls to

ssh stergachis

won’t require that you login as long as the first session is still open.

Don't copy data, use softlinks

Lets say there are some subreads in /mmfs1/gscratch/stergachislab/data/... that you want to use in your project. Don't copy these files, instead use softlinks. e.g.

ln -s /mmfs1/gscratch/stergachislab/data/...subreads.bam /path/to/my/project/data/.

This puts a link to the file in a convenient place for you without copying all the data, and you can use these links like regular files with all your programs 😄 !

Some Unix tools I love

  • Starship is a minimal, blazing fast, and extremely customizable prompt for any shell! Starship: Cross-Shell Prompt
  • lsd, alias ls to lsd for a pretty terminal
  • fd an simpler/faster version of find
  • ripgrep/rg a faster version of grep
  • A whole lot more

See how many jobs you can use on checkpoint

first add this to your .bashrc

alias joblimit=$'squeue  | grep -w R | grep ckpt |  wc -l | awk \'{print "Running Jobs: "$1}\' && sacctmgr show assoc where account=ckpt format=GrpJobs | grep -P "\d+" | awk \'{print "Allowed Jobs: "$1}\''

then

$ joblimit
Running Jobs: 65
Allowed Jobs: 64

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