BAShTools

This repository contains several scripts to improve quality of life in terminal and HPC workflows. Most programs have a basic help screen which can be accessed with the flag -h or --help. While some of the scripts are ready to go out of the box, follow the installation instructions at the bottom of this page for all features to work.

Console IO:

• colours.sh contains ANSI escape strings to change console output colours in the MTools colour scheme. Source this script to access the variables. (Portable)
• out.sh functions to format output to console. Source this script to access the functions (Portable)

SLURM specific

• sq.sh pretty list of all active jobs for a given user. (Intended only for SLURM HPC's)
• sb.sh pretty SLURM job submission.
• wd.sh change to, list, and get paths to working directories that fit the pattern ~/WD_<NUMBER>_<TAGS>. (Portable)
• send2access.sh easily send files to a folder called 'fromEureka' on access.eps.surrey.ac.uk
• mod_run.sh change the SBATCH comments in a run file easily. (Intended only for EUREKA)
• results.sh quickly see the results of a job queued with submit.sh (Portable)

EUREKA Specific

• djvu2pdf.sh converts djvu files to pdf (Intended only for EUREKA).
• usage.sh shows your disk usage for $HOME & $PSCRATCH. (Intended only for EUREKA).
• rogue.sh SSH into recently used nodes to try and identify headless/rogue processes. (Intended for EUREKA).
• send2access.sh SCP files to the access server. Barebones.

Amber + AmberTools specific

• load_amb.sh Load Amber on EUREKA (Intended only for EUREKA)
• load_amb_nwc.sh Load Amber on EUREKA (Intended only for EUREKA)
• amb_avg.sh Produce a PDB with the average coordinates in an Amber MDCRD trajectory.
• amb_stats.sh Parse energy minimisation and other log files. Barebones.
• run_wham.sh Run WHAM to produce free energy barriers from umbrella sampling simulations.

git automation

• allgits.sh display the status of all git repositories in your home directory. (Broken when git directories have spaces)
• newgit.sh easily initialise a new git directory with an automatically generated README.md file and push to GitHub or the University of Surrey's GitLab. Requires careful configuration of this package via the configure.sh script. (Portable)

Others

• directory_exists.sh provides functions to check if directories and files exist.
• authname.sh parses .bib files for author lists
• confucius.py Office wisdom
• loop_this.py <COMMAND> Run any command in an infinite loop.
• rename.sh Batch renaming of using pattern matching.
• table.sh Perl version of the column -t command.

MacOS

• unmount.sh Uses osascript to unmount external drives.

Installation

• To use these tools clone this repository and add the directory to your BASh PATH variable.

git clone https://github.com/mwinokan/MShTools.git

cd MShTools

echo "export MSHTOOLS=$PWD" >> ~/.bash_profile

echo 'export PATH=$MSHTOOLS:$PATH' >> ~/.bash_profile

• Many scripts require Surrey and gitlab credentials. Create the files using configure.sh, see configure.sh -h and comments in script for information.
• wd and other scripts need to be sourced to run, you may wish to add the following alias to your .bash_profile: alias wd='source $MSHTOOLS/wd.sh'
• You may prefer to define aliases for newgit.sh, results.sh, and sq.sh - i.e. alias newgit='bash $MSHTOOLS/newgit.sh'