[Bio-Linux] Cron and Qiime
Cox, Michael J
michael.cox1 at imperial.ac.uk
Mon Oct 4 09:34:46 EDT 2010
Hi Tony P,
Sorry, I did uncomment those lines and rerun backup, but it didn't return anything different from before. I'm pretty sure that I've uncommented the right part of the script (there's only one debug line), but here is a full copy of my backup script as it now stands.
Tony T, is the answer to create a file at /etc/default/backup with the config details that you list?
Thanks Mike
#!/bin/bash
#Fail on errors!
set -e
set -u
#######################################################################
# /etc/cron.daily/backup - a script to backup one hd to #
# another on the same machine, using dump #
# (see the dump man page for details, and #
# http://envgen.nox.ac.uk/envgen/software/archives/000501.html#auto #
# #
# Written by MIT, 20/6/2002 #
# Modified by Dan Swan for Bio-Linux 2.0 17/3/2003 #
# Updated for Bio-Linux 5 by Tim Booth 1/8/2008 #
# Updated to perform Quarterly ETOH backups by Tony Travis 17/7/2009 #
# Updated to dump ext4 fileystems by Tony Travis 19/5/2010 #
#######################################################################
# Source configuration file
CONFIG=/etc/default/backup
if [ -r $CONFIG ]; then
. $CONFIG
fi
#Use basic or ETOH mode?
backup_mode=${MODE:="etoh"}
#Where to backup
backup_destination=${DESTINATION:="/backups"}
#What to backup
backup_filesystems=(${FILESYSTEMS:="/home" "/var" "/usr"})
#Compression scheme. For large drives bzip2 is probably too slow.
compression_mode=${COMPRESSION:="z"}
# get the date
day=`date +%a`
month=`date +%b`
dom=`date +%d`
#Dump level can be set on command line or by today's date.
if [ -n "$*" ]; then
level="$1"
elif [ "$backup_mode" == "etoh" ] ; then
# Quarterly Enhanced Towers of Hanoi
if [ $day == "Sun" ]; then
if [ $dom -le 7 ]; then
case $month in
"Jan" | "Apr" | "Jul" | "Oct") level=0 ;;
*) level=1 ;;
esac
elif [ $dom -le 14 ]; then
level=3
elif [ $dom -le 21 ]; then
level=2
elif [ $dom -le 28 ]; then
level=4
elif [ $dom -le 31 ]; then
level=3
fi
else
case $day in
"Mon") level=6 ;;
"Tue") level=5 ;;
"Wed") level=8 ;;
"Thu") level=7 ;;
"Fri") level=9 ;;
"Sat") level=8 ;;
esac
fi
elif [ "$backup_mode" == "basic" ] ; then
# dump is 9 any day but Sunday
if [[ $day == "Sun" ]]; then
level=0
else
level=9
fi
else
echo "ERROR: Unknown backup mode and no level specified"
exit 1
fi
# dirs to back up - used to be:
#backups=(hda1 hda2 hda5 hda6)
#But now I need to be a bit more sophisticated.
#List filesystems to back up and use mount to find where they are.
backups=()
for fs in "${backup_filesystems[@]}" ; do
device=`mount | egrep "[^[:space:]]+ on $fs type ext[234]" | awk '{print $1}'`
if [ "$device" != "" ]; then
backups[${#backups[@]}]=$device
fi
done
#DEBUG
echo ${backups[@]} $level $compression_mode
exit
# if backup drive is already mounted then try to unmount it first.
# if this is in use the step will fail and exit
/bin/mount | grep -q "/backups" && /bin/umount /backups 2>/dev/null
# mount necessary drive - must be listed
# in /etc/fstab in order to be mounted
/bin/mount "$backup_destination" 2>/dev/null || exit 0
# dump each directory, one at a time
for item in "${backups[@]}"; do
basename=`basename $item`
#sync or swim
sync
/sbin/dump -"$level" -"$compression_mode" -n -u -f "$backup_destination/$basename.bak.$level" "$item"
done
# umount drive
/bin/umount "$backup_destination"
On 4 Oct 2010, at 12:00, <bio-linux-request at nebclists.nerc.ac.uk> wrote:
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Today's Topics:
1. Re: Cron and Qiime (Tony Travis)
----------------------------------------------------------------------
Message: 1
Date: Sun, 03 Oct 2010 16:31:49 +0100
From: Tony Travis <a.travis at abdn.ac.uk>
Subject: Re: [Bio-Linux] Cron and Qiime
To: bio-linux at nebclists.nerc.ac.uk
Message-ID: <4CA8A1E5.6040006 at abdn.ac.uk>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 30/09/10 15:12, Anthony Pemberton wrote:
Mike,
OK cron is running. This looks like the problem I encountered with the script /etc/cron.daily/backup - under
#What to backup
backup_filesystems=(${FILESYSTEMS:="/home" "/home1"})
Note the use of the double quotes around the partitions you want to backup (these are the mount points). If I remember correctly, the quotes were missing and are now required. I think that is why the script is failing. The default config is a "red-herring" because what the script is saying is: if the file exists read it, if not continue.
The way to quickly test the script after editing is to run it from the command line eg.
% sudo -i
# cd /etc/cron.daily
# ./backup
and see what happens. Use of echo statements in shell scripts like this helps to debug,
Hello, Tony.
Tim added my changes to bio-linux-backups, but I have also noticed
problems if an "/etc/default/backup" file is absent. Sorry, I should
have posted something to the list.
I use these defaults (from Bio-Linux 5) for our NBX's:
# @(#)/etc/default/backup 2009-07-17 A.J.Travis
#
# Bio-Linux 5.0 backup configuration
#
# Where to backup
#DESTINATION="/backups"
# What to backup
#FILESYSTEMS="/ /home /var /usr"
FILESYSTEMS="/ /home"
# Compression scheme. For large drives bzip2 is probably too slow.
#COMPRESSION="z"
HTH,
Tony.
--
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt
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End of Bio-Linux Digest, Vol 36, Issue 3
****************************************
Mike Cox
Research Associate
Centre for Respiratory Infection
National Heart Lung Institute
Royal Brompton Campus
Guy Scadding Building
London SW3 6LY
michael.cox1 at imperial.ac.uk
http://www1.imperial.ac.uk/medicine/people/michael.cox1/
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