Appendix: Bash

Bash is a scripting langauge, used on Unix machines. You might need the following commands.

Make a bash file executable

This allows you to execute script files or change the content of a file with shell:
chmod u+x name_of_file.sh
chmod means change mode (make it executable), u means for all users and x means executable (+ is the liaison key word).
You can then run the script by typing ./nameoffile.sh.

Some bash commands

To change the content of a file use sed:
sed -i '143s/*/text_to_put_on_the_line' name_of_file
sed stands for stream editor. -i means it will save the file with the modifications. -s is for substitution. This will act on line 143 only.
You can also substitute a word (snetence) with another sentence
sed 's/sentenceToChange/newSentence/g' myfile.txt
Stream editor is a convenient tool that can be used for other tasks. For example, filtering lines of a text file (and copying them into another text files).
sed -n '1p' textfile.txt > textfile2.txt
-n stands for filtering and the p after the 1 for print. To copy only even lines, do
sed -n '2~2p' textfile.txt > textfile2.txt
The '2~2' means start at line two and keep every line by step of 2. TO keep lines 5 to 10 you can use '5,10p'. To keep several diferent ranges of lines (line 1 to 10 and line 21 to 30) use
sed -n -e '1,10p' -e '21,30p' textfile.txt > textfile2.txt

commands

Adding the symbol & at the end of a line will have the job run in the background, so the script will continue to the next line. It is a convenient way to launch several jobs on a cluster, for example.