Scripts for Linux

Last Updated 2020-10-29 by Adam Lu

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Scripts only in this directory

Note: Regardless of location, these scripts could be run with the command:

bash ~/Settings_Linux/scripts/<scriptname>.sh

• backup_scripts: Older versions of many scripts
• backup_settings.sh: Backs up /etc, /proc files and cron jobs to the backup_settings folder
  • Note: To add directories or files to back up, edit the dirsToBackup or filesToBackup array
• setup_binfiles.sh: Copies shell scripts from the current directory to /usr/local/bin/
  • Note: To add files, edit the filesToStore array and update it in store_binfiles.sh as well
• store_binfiles.sh: Copies shell scripts from /usr/local/bin/ to the current directory
  • Note: To add files, edit the filesToStore array and update it in setup_binfiles.sh as well
• store_dotfiles.sh: Copies configuration files from the home directory to the current directory and append user name
  • Note: To add files, edit the filesToStore array and update it in setup_dotfiles.sh as well

Scripts copied to /usr/local/bin

Note: Regardless of location, these scripts could be run with the command:

bash <scriptname>.sh

Note: You can edit these scripts here, then update them in /usr/local/bin with the commands:

cd ~/Settings_Linux
git_update
bash setup_binfiles.sh

• create_new_script.sh: Creates a new shell script with a given name starting from template.sh (see vi_new_script.sh, nano_new_script.sh)

• vi_new_script.sh: Creates a new shell script with a given name starting from template.sh and opens it with the vim editor

• nano_new_script.sh: Creates a new shell script with a given name starting from template.sh and opens it with the nano editor

• git_update.sh: Syncs .git local repository with remote repository, commits new changes then syncs with remote repository again

• git_all_update.sh: Runs git_update.sh on all blabuva repositories

• filetypes.sh: Returns file types for all files in a given directory

• ls_numfiles.sh: Lists the number of files in each subdirectory of a given directory

• modlunit_all.sh: Runs modlunit (a NEURON program for checking code and units) for all .mod files in a given directory

• cleanup_cache.sh: Cleans up cached folders that are no longer needed

• cleanup_swap.sh: Cleans up swap partition and cached memory

• swap2ram.sh: Moves swap to RAM if possible (see cleanup_swap.sh)

• setup_all_homedirs.sh: Sets up all home directories

• setup_homedir.sh: Sets up .desktop files, configuration files and links and removes unnecessary files in a user’s home directory

• setup_links.sh: Sets up links for a user’s home directory

  • Note: To add directories to link, edit the dirsToLink array

• setup_desktopfiles.sh: Copies useful .desktop files to a user’s Desktop directory

  • Note: To add .desktop files, edit the usrSharePrograms array

• setup_dotfiles.sh: Copies configuration files from the current directory to a user’s home directory

  • Note: To add files, edit the filesToStore array and update it in store_dotfiles.sh as well

• backup_to_chalkboard.sh: Backs up data from other computers to chalkboard

  • Note: To add directories, edit the sourceDirs and destDirs array simultaneously

• backup_to_fishfish.sh: Backs up data from other computers to fishfish

  • Note: To add directories, edit the sourceDirs and destDirs array simultaneously

• notice_blanimal.sh: Generates blanimal Notice and sends it to everyone in an email list based on a Google spreadsheet

• notice_blanimal_for_testing.sh: Generates an email (blanimal Notice) and send to Adam or Brian

• notice_census_today.sh: Generates today’s primary and backup census takers

• notice_census_future.sh: Generates primary and backup census takers for the following week

• notice_colony_today.sh: Generates primary and backup colony checkers for today

• notice_colony_future.sh: Generates primary and backup colony checkers for the following week

• notice_wean.sh: Generates wean information for today

• notice_genotype.sh: Generates genotype information for today

• combine_all_current_notebooks.sh: Calls combine_current_notebooks.sh for many users

  • Note: To add the name of a student, edit the gradNames or undergradNames array

• combine_current_notebooks.sh: Concatenates all pdf files under /media/shareX/type_books/name into a single pdf file called name_notebook.pdf, then upload the file to the AWS S3 bucket. This file is placed under /home/grads if type == “grad” and under /home/undergrads if type == “undergrad”. The concatenation is defined in combine_notebooks.sh)

• combine_notebooks.sh: Concatenates all pdf files under inputDir into a single pdf file. The concatenation goes in reverse order according to YYYYMMDD, assuming that the original files are named as MMDDYYYY.pdf

• notice_happy.sh: Sends emails for happy hour for every nDaysBefore based on Google spreadsheets

  • Note: To change the frequency of emails, edit the nDaysBeforeAll array

• happy_message_maker.sh: Makes a message for happy hour and places it into messagePath

• notice_blunch.sh: Sends emails for blunch for every nDaysBefore based on Google spreadsheets

  • Note: To change the frequency of emails, edit the nDaysBeforeAll array
  • Note: To add people to the email list, edit the names and emails array

• blunch_message_maker.sh: Makes a message for blunch and places into messagePath

• aws_post_files.sh: Posts files to the webfiles directory on AWS

  • Note: To add files to post, edit the filesToPost array

• aws_update_dirs.sh: Updates directories to AWS

  • Note: Needs to be cleaned

• aws_papers_updater.sh: Uploads PDF files to AWS and creates HTML chunk code

• wp_papers_html_email.sh: Sends emails for updated WordPress HTML code

• wp_papers_html_writer.sh: From a given inFolder, uploads new PDF files and generate WP HTML code

• create_readme_from_links.sh: Creates a README.md from a directory of .url links

• create_readme_from_images.sh: Creates a README.md for a directory of images

• create_readme_from_mscripts.sh: Creates a README.md from a directory of .m scripts

• create_readme_from_files.sh: Creates a README.md for a directory based on the contents

• create_readme_from_weblinks.sh: Creates a README.md for a directory of .url weblinks

• watch_all_readmes.sh: Start automatic updates for README.md files in designated directories

• watch_readme.sh: Watches the README.md from a directory

• mount_all_disks.sh: Mounts all detected disks according to their label

• adams_commands.sh: Custom commands available in the command line by Adam Lu Note: Please check out the documentation before each function name for more detailed usage
  • plier: Multiplies together a sequence of numbers
  • iseven: Returns 0 if an integer is even or 1 if an integer is not even
  • nevens: Prints the number of even integers within a sequence of integers
  • howodd: Prints the percentage of odd integers in a sequence of integers
  • fib: Prints the number of Fibonacci numbers specified
  • range: Takes an integer as an argument and prints all of the integers
  • extremes: Prints the maximum and minimum values of a sequence of numbers
  • rand_word: Prints a random word from the built-in dictionary
  • tagged_copy: Creates a tagged copy of file(s)
  • dated_copy: Creates a dated copy of file(s)
  • timed_copy: Creates a time-stamped copy of file(s)
  • timed_log: Creates a time-stamped .log file from standard input
  • ismember: Returns whether a string is contained in an array
  • idxmember: Returns the index of a string in an array
  • str_prepend: Prepends a string to each string in an array
  • str_append: Appends a string to each string in an array
  • fileext: Returns the file extension of a file
  • filetype: Returns a message about the file type
  • standardize_path: Returns a full path with no terminal /
  • url: Retrieves the URL from a .url file
  • add_IP: Adds an IP address to the firewall for ports
  • checkcp: Copies a file only if two files are different
  • checkrm: Checks if a file exists before removing
  • archive: Backs up files or directories with rsync or pseudofiles with checkcp
  • create_backup_path: Creates a backup dir or file name based on original path
  • create_sample_path: Creates a sample file name based on original path
  • get_user_ID: Retrieves the user ID of a user
  • get_group_ID: Retrieves the group ID of a user
  • get_full_name: Retrieves the full name of a user
  • chowner: Changes owner and group of a file based on username
  • chmodifowner: Changes permissions of a file if the current user is the owner
  • checkdir: Checks if a directory exists and creates it if not
  • spaces2dashes: Converts spaces to dashes
  • all_image_files: Returns a list of image files in a directory
  • is_image: Checks if a file is an image
  • is_weblink: Checks if a file is an weblink
  • is_mscript: Checks if a file is a MATLAB script
  • is_shscript: Checks if a file is an shell script
  • is_textfile: Checks if a file is a text file or a log file
  • is_csvfile: Checks if a file is a csv file
  • is_markdown: Checks if a file is a markdown file
  • is_folder: Checks if a file is an existing directory
  • is_file: Checks if a file is an existing file
  • is_filetype: Checks if a file is a given filetype
  • topcommand: Calls top for a particular command
  • htopcommand: Calls htop for a particular command
  • killcommand: Kills all processes for a particular command
  • print_readme_header: Prints the header for a README.md file
  • update_readme_header: Updates the header for a README.md file
  • get_description_from_mscript: Get the description from a .m script
  • get_description_from_shscript: Get the description from a .sh script
  • get_description_from_filename: Get the description from a file name
  • grep_line_numbers: Finds the line numbers that match a pattern in a file
  • get_git_repository_name: Retrieves the git repository the file is contained in
  • bulk_subtract: Subtract a number from a list of numbers
  • bulk_add: Add a number to a list of numbers
  • template_function: A template function to modify from
• TODO
• create_readme_from_images.sh: Creates a README.md for a directory of images
• get_timestamps.py
• notice_undergrad_tasks.sh: Sends emails for undergrad tasks
• sample scripts
• git_all_update.sh: Runs git_update.sh on all blabuva repositories
• git_update.sh: Syncs .git local repository with remote repository, commits new changes
• backup_to_fishfish.sh~
• copy_and_rename_recordings.sh: Copy and rename recordings (.abf files) based on markdown notes Note: Please check out the documentation before each function name for more detailed usage
  • copy_and_rename_recordings_helper: copies and rename recordings
• create_matlab_links.sh: TODO: This is a template file for a new shell script Note: Please check out the documentation before each function name for more detailed usage
  • functionName: TODO