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ResBaz mini-session Introduction to Command-line tools (Day2)

A lesson on how to set-up your computer so you can use command-line tools from anywhere, and you don't lose them buried in your direcotries.

Example tool used: https://www.cog-genomics.org/plink2

If you try and run this tool from outside the folder it is saved in (before set-up) you will get an error

bash: plink: command not found...

So, let's fix that!

  • Make yourself a safe place to keep everything
      mkdir ~/MyTools
      mkdir ~/MyTools/bin

  • From now on when you download a command-line tool save it in the MyTools directoy - that way you won't lose it or delete it

  • To run that program from anywhere we need to follow two/three quick set-up steps

    • make a symbolic link to your new tool - this link should live in the ~/MyTools/bin folder you just made
    • symbolic links need full file paths (not relational file paths - as in full/path/to/this/file vs ../this/file - ~ counts as a full path)

  • set-up your bash environment to always search for tools in your ~/MyTools/bin folder (as well as the places it normally searches)

    • To do this make a .bashrc file - a .bashrc file is a file that runs (automatically) every time you open a new terminal window. It's purpose is to provide a place where you can set up variables, functions and aliases, define your prompt/other settings.
nano ~/.bashrc
   PATH=${PATH}:/Users/myusername/MyTools/bin
# save and exit nano
  • refresh your bash environment to read from that file
source ~/.bashrc
  • on a mac you need to complete one final step, linking your .bashrc file to your .bash_profile file - if you do not do this you will need to run source ~/.bashrc everytime you open a new Terminal session
    • here are two possible ways to do this
ln -s ~/.bashrc ~/.bash_profile

OR [this is useful if your .bash_profile file already has something in it]

nano ~/.bash_profile
   source ~/.bashrc
# save and exit nano
  • now try it! go to any directory, type in the name of the tool you just installed (eg. plink). Does it run?

NEXT TIME YOU DOWNLOAD A NEW TOOL TO USE YOU ONLY NEED TO DO THE SYMBOLIC LINK STEP TO MAKE IT AVAILABLE FROM ANYWHERE

  • if you have multiple tools in the same folder that you want to set up symbolic links to, use a for loop
cd ~/MyTools/folder/with/lots/of/tools
for tool in $(ls *); do ln -s ~/MyTools/folder/with/lots/of/tools/$tool ~/MyTools/bin/${tool}; done

why is any of this important/useful?

  • if you need to access tools via other scripts it is much easier and tidier to only use the tool_name than the full file path
  • you can also make a group tools folder so everyone in your group uses the same tools/versions - all have .bashrc pointing to the same place; this is relevant to working on servers that everyone can access - not so much working on your own computer.