Shell

Colors in less

Use the -r or -R option. Sometimes the previous command needs a parameter make sure the output includes color codes.

tree -C | less -R
ls --color | less -R
grep --color=always | less -R

Avoid killing ssh jobs

nohup function (apparently).

Set memory limits for a terminal session

ulimit -Sv 10000000

With 10000000 here being the maximum virtual memory in bytes.

Custom prompt

To shorten the prompt in my terminal, I tweaked this paragraph in my ~/.bashrc:

if [ "$color_prompt" = yes ]; then
    PS1='[${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u\[\033[00m\] \[\033[01;34m\]\W\[\033[00m\]]\$ '
else
    PS1='${debian_chroot:+($debian_chroot)}\u \W\$ '
fi

\u is the username and \w/\W is the working directory (directory name/full path). Compared to the default, I just added flanking [/], a space instead of a :, and to use the directory name instead of the full path.

Bash & Pipes

Add headers with cat

cat file.txt | cat headers.txt -

Remove empty directories

find . -type d | xargs rmdir

Git add all untracked files

git st -s | grep '??' | cut -f2 -d ' ' | xargs git add

Open recent PDFs

find pdf -mtime -1 | xargs evince

AWK

• /pattern/ or $2~/pattern/
• Split a string into an array: split($3, a, ",")
• Substitute pattern in string: gsub('pattern', 'replacement', $4)
• Capture group in string regexp using match($2, /xxx(.*)yyy/, a); print a[1]'
• Set output separator to tabs: BEGIN{OFS="\t"} (same idea for FS, RS, ORS)
• GNU Manual
• Sarah’s in-house join: awk -v fileRef=file.with.info 'BEGIN{while (getline < fileRef >0){info[$1]=$2}} {print $0, info[$1]}' input

Perl one-liners

Inspired from these: Catonmat, Ksplice

• -p run command on each line and print line.

• -n run command on each line but don’t print line.

• -i operates on the file in-place, i.e. updating the input file.

• -a split the lines by white spaces into a @F array (-F to choose the separator)

• -l removes the trailing new line, and adds it back if -p is used.

• $_ contains the line.

• $. contains the line number.

• Replace text line-by-line in a file: perl -pe 's/you/me/g'

• Replace text if line contains foo: perl -pe 's/you/me/g if /foo/

• Replace text line-by-line with regexp: perl -pe 's/ID(\d+)/$1/g'

• Operations on a CSV file: perl -F, -ane 'print $F[3]+$F[8]

• Operations on a CSV file and print at the end: perl -F, -ane $t+=$F[3]+$F[8]; END{print $t} %

• Print matches from regular expression: perl -ne 'print "$1\n" if /foo=([^;]*)/'

Variables

To remove a specific prefix/suffix from a variable name:

foo=${foop#prefix_to_remove}
foo=${foos%suffix_to_remove}
foo=${oof/motif_to_pattern/by_this_pattern/}

Looping

Loop across lines of a file:

while read in_line
do
    command $in_line
done < lines.txt

If Then Else

A simple example:

if [ $VAL == "YEP" ]; then
	echo "It's a yes!"
else
	echo "No no no :("
fi

Or with multiple conditions:

if [ $VAL == "YEP" ] && [ COND ]; then
	echo "It's a yes!"
else
	echo "No no no :("
fi

The spacing is quite important, and the conditions can be built with:

• -eq equal to.
• -ne not equal to.
• -lt less than.
• -le less or equal than.
• -gt great than.
• -ge great or equal than.
• -s file exists and not empty.
• -f file exists and not directory.
• -d directory exists.
• -x file executable.
• -w file writable.
• -r file readable.

Sound problems

I touched something my headphones sometime bug (white noise and bad sound quality). This fixes it (in my ~/.bashrc):

alias soundfix='amixer -c PCH cset "name=Headphone Mic Boost Volume" 1'

Mount server

I created a directory sftp (I don’t know why I choose this name…anyway) and mount the root of the different servers there. Eventually I created a symbolic link at the root of my computer to point there so that paths like /gs/projects/... work directly, as if in the cluster.

To mount a server I use the following command:

sshfs jmonlong@guillimin.hpc.mcgill.ca:/ /Users/jeanmonlong/sftp/guillimin -ovolname=NAME

Setup WD Elements external hard drive

By default the disk is formatted in NTFS, which OSX could read only. To write, the solution that worked for me was to add this line to /etc/fstab:

LABEL=Elements none ntfs rw,auto,nobrowse

Note: If there are spaces in the label, replace them by \040.

The disk can then be accessed through the Volumes folder (/Volumes).