pnsinha

#!/bin/bash

# Variables
USERNAME="pnsinha"
SSH_KEY="ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC9p/5ob6qOD55c+DdYTVDLpanxoCULNJAaNZIr1rNv9bdw7yaq1Ow3TbYrLmcV0ZVKnCQM/ZRa//tM/ybx7zbFQkh8aKwZog0f84+ImeqNoO5NfodoiGbQMEv+OKxXo4UaXO3lJIVIe1z5brBatxSOuTHM0oIeWowUKPURX5oCYmeekivseWFHJ+DGB+cmlmtntR8G1pXrMFv7+T+j3H8F+PI6RREZvftUj9eZiGKstFIGuSRzkCkqwWBXzwBrl8FZgZ/a0eA2V59PHt0C3XOMYGfBXBrKinV79Poc9Sddn8sodnoO8t46CjROR58+ADGSZRXjtH+84Hk3oXYzbXCZ parma@DESKTOP-UCGIS"

# Create a new user
echo "Creating user $USERNAME..."
sudo useradd -m -s /bin/bash "$USERNAME"

pnsinha

python /software/alphafold3.0-el8-x86_64/alphafold3/run_alphafold_test.py \
--db_dir /software/alphafold3.0-el8-x86_64/databases \
--output_dir /scratch/midway3/$USER/alphafold3_output \
--model_dir /software/alphafold3.0-el8-x86_64/params \
--run_data_pipeline \
--run_inference

pnsinha

Overview of the XDG Base Directory Specification

The XDG Base Directory Specification provides guidelines for where applications should look for configuration files, data files, and cache files in a user's environment. This specification aims to improve the organization of user files and reduce clutter in the user's home directory.

1. Base Directories: The specification defines several base directories that applications should use:
   • $XDG_CONFIG_HOME: This is the directory where user-specific configuration files should be stored. If this variable is not set, the default is ~/.config.
   • $XDG_DATA_HOME: This directory is for user-specific data files, defaulting to ~/.local/share if not set.
   • $XDG_CACHE_HOME: This is where user-specific non-essential data files (cache) should be stored, defaulting to ~/.cache.

• $XDG_STATE_HOME defines the base directory relative to which user-specific state files should be stored. If $XDG_STATE_HOME is either not set or empty, a def

pnsinha

Tool Name	Description	Key Features	Use Cases
scp	A command-line tool for securely copying files between hosts using

pnsinha

#!/usr/bin/expect -f

# Set timeout for the script
set timeout 60

# Define variables for the second server
set my_server "midway3.rcc.uchicago.edu"
set my_username "pnsinha"
set my_password "your_password_here"  ;

pnsinha

Variable	Default Value
%SystemDrive%	C:
%ProgramFiles%	C:\Program Files
%AppData%	C:\Users{username}\AppData\Roaming
%LocalAppData%	C:\Users{username}\AppData\Local
%UserProfile%	C:\Users{username}
%UserName%	{username}
%COMPUTERNAME%	{computername}
%PATH%	C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;{plus program paths}

pnsinha

ldd /software/R-4.2.1-el8-x86_64/lib64/R/library/*/libs/*.so \
| egrep '(so:$|not found)' > ~/R-4.2.1-el8-x86_64/

pnsinha

%runscript
  exec R "${@}"

%post
  export TZ="America/Chicago"
  ln -snf /usr/share/zoneinfo/$TZ /etc/localtime && echo $TZ > /etc/timezone

  dnf makecache --refresh
  dnf install -y tzdata gnupg2 glibc-langpack-en

pnsinha

1) ==== Autossh using systemd ====

Example from

https://gist.github.com/drmalex07/c0f9304deea566842490

2) =============

Install autossh

pnsinha

#https://unix.stackexchange.com/questions/43957/using-rsync-to-move-not-copy-files-between-directories

#!/usr/bin/bash

echo -e "Would you like to use a relative path to your source?[y/n?]\n"
read ans
if [[ $ans == y ]]; then
    echo -e "Relative source?\n"
    read source
    source="`pwd`/$source"