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Notes about open source software, computers, other stuff.

Tag: Bash

Using rsync to backup a ZFS file system to a remote Synology Diskstation

30 October 2014 / / 1 Comment

Some time ago I moved from using LVM to using ZFS on my home server. This meant I also had to change the backup script I used to make backups on a remote Synology Diskstation. Below is the updated script. I also updated it such that it now needs a single command line argument: the hostname of the Diskstation to backup to (because I now have two Diskstations at different locations). If you want to run this script from cron you should set up key-based SSH login (see also here and here).

#!/bin/bash
#
# This script makes a backup of my home dirs to a Synology DiskStation at
# another location. I use ZFS for my /home, so I make a snapshot first and
# backup from there.
#
# This script requires that the first command line argument is the
# host name of the remote backup server (the Synology NAS). It also
# assumes that the location of the backups is the same on each
# remote backup server.
#
# Time-stamp: <2014-10-27 11:35:39 (L.C. Karssen)>
# This script it licensed under the GNU GPLv3.
 
set -u
 
if [ ${#} -lt 1 ]; then
    echo -n "ERROR: Please specify a host name as first command" 1>&2
    echo " line option" 1>&2
    exit -1
fi
 
###############################
# Some settings
###############################
# Options for the remote (Synology) backup destination
DESTHOST=$1
DESTUSER=root
DESTPATH=/volume1/Backups/
DEST=${DESTUSER}@${DESTHOST}:${DESTPATH}
 
# Options for the client (the data to be backed up)
# ZFS options
ZFS_POOL=storage
ZFS_DATASET=home
ZFS_SNAPSHOT=rsync_snapshot
SNAPDIR="/home/.zfs/snapshot/$ZFS_SNAPSHOT"
 
# Backup source path. Don't forget to have trailing / otherwise
# rsync's --delete option won't work
SRC=${SNAPDIR}/
 
# rsync options
OPTIONS="--delete -azvhHSP --numeric-ids --stats"
OPTIONS="$OPTIONS --timeout=60 --delete-excluded"
OPTIONS="$OPTIONS --skip-compress=gz/jpg/mp[34]/7z/bz2/ace/avi/deb/gpg/iso/jpeg/lz/lzma/lzo/mov/ogg/png/rar/CR2/JPG/MOV"
EXCLUSIONS="--exclude lost+found --exclude .thumbnails --exclude .gvfs"
EXCLUSIONS="$EXCLUSIONS --exclude .cache --exclude Cache"
EXCLUSIONS="$EXCLUSIONS --exclude .local/share/Trash"
EXCLUSIONS="$EXCLUSIONS --exclude home/lennart/tmp/Downloads/*.iso"
EXCLUSIONS="$EXCLUSIONS --exclude home/lennart/.recycle"
EXCLUSIONS="$EXCLUSIONS --exclude _dev_dvb_adapter0_Philips_TDA10023_DVB*"
 
 
 
###############################
# The real work
###############################
 
# Create the ZFS snapshot
if [ -d $SNAPDIR ]; then
    # If the directory exists, another backup process may be running
    echo "Directory $SNAPDIR already exists! Is another backup still running?"
    exit -1
else
    # Let's make snapshots
    zfs snapshot $ZFS_POOL/$ZFS_DATASET@$ZFS_SNAPSHOT
fi
 
 
# Do the actual backup
rsync -e 'ssh' $OPTIONS $EXCLUSIONS $SRC $DEST
 
# Remove the ZFS snapshot
if [ -d $SNAPDIR ]; then
    zfs destroy $ZFS_POOL/$ZFS_DATASET@$ZFS_SNAPSHOT
else
    echo "$SNAPDIR does not exist!" 1>&2
    exit 2
fi
 
exit 0

Using ‘expect’ to distribute files among users

5 August 2014 / / 0 Comments

I’m currently teaching at the Summmer School in Statistical Omics in Split, Croatia. A great experience!

Because of the computations involved in the project work, we have access to a server. However, since the machine is part of a university cluster, I haven’t been given full root permissions (in fact, I’m only allowed to use sudo to install packages).

Now, the problem I had to solve was that I needed to distribute a certain file (.Renviron) to each student’s home directory. Normally I’d use sudo to do that, but the admin hadn’t allowed me to use cp via sudo. Furtunately, I had a list of user names and passwords for the students (because I had to distribute those), so I thought I’d use su - to change to each student’s account and copy the file, something along the lines of

echo PASSWORD | su -

and then loop over each account. Unfortunately, while testing the script I found out it wouldn’t work since su complained:

su: must be run from a terminal

Then I remembered the expect tool, which executes commands based on what it ‘sees’ on the command line. In this case I wanted it to enter the password at su‘s prompt. This is the expect script I came up with, it accepts two command line arguments, the user name and the password:

#!/usr/bin/expect -f
 
set user [lindex $argv 0]
set pass [lindex $argv 1]
 
spawn su - $user
expect "Password: "
send "$pass\r"
expect "$ "
send "cp -i /common/WORK/school/lennart/.Renviron .\r"
expect "$ "
send "ls -l .Renviron\r"
expect "$ "
send "exit\r"

The script was wrapped in the Bash script that I had already written:

#!/bin/bash
#
# This script is used to copy files from this directory to the
# home directories of the users listed in $USERFILE.
 
USERFILE=accounts.txt
SRCFILE=/common/WORK/school/lennart/.Renviron
 
while read user passw; do
    ./copy_file_to_users.expect $user $passw
done < $USERFILE

Fixing colours in git output after upgrading to Ubuntu 14.04

5 May 2014 / / 1 Comment

After upgrading my Ubuntu 13.10 installation to 14.04, I noticed that the output of several git commands (e.g. git diff and git log) didn’t show colours as they used to, but showed ESC[ ANSI codes instead.
A quick internet search lead to this post on unix.stackexchange.com where the LESS environment variable was ‘blamed’. Indeed, I have my LESS variable (re-) defined in my .bashrc and .zshrc files.

The solution was to add -R to the environment variable, which allows raw control characters to be displayed. I now have the environment variable defined as:

LESS='--quiet -X -F -R'

Replacing a character in a Bash variable name

4 December 2013 / / 0 Comments

Today I needed to replace a : in a bunch of file names with a -, so I wanted to write a Bash for-loop to do just that. I vaguely remembered that you can do character replacements within variables, but couldn’t remember the details.

This is how it’s done:

for filename in *; do
    mv "$filename" "${filename/:/-}"
done

I put the variables in double quotes, because the file names contained spaces.

Exit a Bash script if an error occurs

5 July 2013 / / 0 Comments

Last week I found out that a Bash script I wrote to do some data QC gave me a false sense of security: a script continues even if one (or more) of the statements in the scripts fails (with an exit status not equal to 0). It turned out that for some of the data sets the QC wasn’t done correctly because I didn’t check the exit status after each step.

My first thought was: oh boy, that means I have to check $? for every step. That means a lot of repetitive code to write! Luckily my colleague came with the answer: add

set -e

at the top of you Bash script and the script will fail if one of its statements fails (for the fine print see the top answer in this is StackOverflow post).

Embedding album art in FLAC files

31 July 2011 / / 5 Comments

I recently wanted to add cover art to my collection of FLAC-encoded audio files. I wrote the following simple script to help me automate the process. Running this script in a given directory (I group my music in directories per artist, followed by a subdirectory for each album) with the name of the album art image file name as argument then automatically embeds the image in the FLAC/Vorbis tag.

#!/bin/bash
#
# This script embeds a given image (usually .jpg) as album art in the
# FLAC files in the present directory (and its subdirectories).
#
# Time-stamp: <2011-07-31 20:43:23 (lennart)>
 
coverart=$1
 
find . -name "*.flac" -print0 |xargs -0 metaflac --import-picture-from="$coverart"

Enable incremental-search-forward in Bash

26 November 2010 / / 0 Comments

I just read Ruslan Spivak’s blog posting on how to get Ctrl-s (which is bound to incremental-search-forward in Emacs) working to search incrementally through the command history in Bash.

Normally this behaviour is shadowed by a terminal flow-control key binding. To turn that off and ‘reveal’ the search-forward function, simply type

stty -ixon

(of course, by adding this line to your ~/.bashrc file makes it permanent).

Great to get this working! Thanks Ruslan.

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