[Bio-Linux] Cron and Qiime
Cox, Michael J
michael.cox1 at imperial.ac.uk
Thu Sep 30 08:03:16 EDT 2010
Thanks so much for your help Anthony,
cron is running:
root 1267 1 0 Sep28 ? 00:00:00 cron
and sudo start cron gave: cron is already running.
Checking cron.daily/backup the backup destination is backup_destination=${DESTINATION:="/backups"}
and checking fstab, this does seem to exist and to be mounted:
/dev/sdb1 /backups ext4 defaults,noauto 0 2
However cron.daily/backup also lists a config file:
# Source configuration file
CONFIG=/etc/default/backup
if [ -r $CONFIG ]; then
. $CONFIG
fi
Which doesn't exist in /etc/default/backup - could this be the source of the problem? mount /backups gives the same empty Lost+found directory.
Thanks to you too Bela,
Helpdesk it is, non-virtualbox qiime looks to be a slippery customer :)
Cheers
Mike
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Today's Topics:
1. Cron and Qiime (Cox, Michael J)
2. Re: Cron and Qiime (Anthony Pemberton)
3. Re: Cron and Qiime (Tiwari, Bela)
----------------------------------------------------------------------
Message: 1
Date: Wed, 29 Sep 2010 15:40:36 +0100
From: "Cox, Michael J" <michael.cox1 at imperial.ac.uk>
Subject: [Bio-Linux] Cron and Qiime
To: "bio-linux at nebclists.nerc.ac.uk" <bio-linux at nebclists.nerc.ac.uk>
Message-ID:
<E11406C7CCAD0847AFC5C6100B004FDB2270AFA165 at ICEXM5.ic.ac.uk>
Content-Type: text/plain; charset="us-ascii"
Dear All,
Hope you can forgive two, probably quite naive, questions.
1. I have recently installed Biolinux 6 as sole operating system on our new workstation. I have two hard drives and so have used the 'setup backup disk' utility to format the second for automated backups. The NEBC website gives details of how to restore back-ups, but I'd like to check to see whether they're actually being made nightly. su-ing to root I can access the second hard drive, but the only directory, Lost+Found is empty. Does this mean that cron.daily isn't running and how can I remedy this? I also have packages to update in the morning, which should also be run automatically by cron.daily, adding to my suspicions.
2. Has anyone attempted a native install of Qiime and its dependencies on Biolinux 6? http://qiime.sourceforge.net/install/install.html
I am having an issue getting various programs that are present to be recognised. I am editing .customrc in /etc/zsh/zshrc.d in order to set paths in zsh, but it doesn't seem to be working - is this the correct file to edit?
Thanks for your help
Mike Cox
------------------------------
Message: 2
Date: Wed, 29 Sep 2010 16:23:26 +0100
From: Anthony Pemberton <A.J.Pemberton at bham.ac.uk>
Subject: Re: [Bio-Linux] Cron and Qiime
To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk>
Message-ID:
<3A5B0BBDAF00724AB5F10155650102300216806BC4 at LESMBX1.adf.bham.ac.uk>
Content-Type: text/plain; charset="us-ascii"
Mike,
I can only help with item 1:
First check to see whether cron is running
% ps -ef | grep cron | grep -v grep
If not you will need to set this running:
% sudo start cron
Cron reads /etc/crontab which starts anacron at the appropriate times, running cron.daily. If the backup disk is empty, either the backup is being misdirected or it is not occurring. See if you can see where the backup if it is occurring, is going by looking at:
/etc/cron.daily/backup
I am assuming the latest 'setup backup disk' utility sets this file up correctly and sets cron running.
Regards,
Tony Pemberton
-----Original Message-----
From: bio-linux-bounces at nebclists.nerc.ac.uk [mailto:bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Cox, Michael J
Sent: 29 September 2010 15:41
To: bio-linux at nebclists.nerc.ac.uk
Subject: [Bio-Linux] Cron and Qiime
Dear All,
Hope you can forgive two, probably quite naive, questions.
1. I have recently installed Biolinux 6 as sole operating system on our new workstation. I have two hard drives and so have used the 'setup backup disk' utility to format the second for automated backups. The NEBC website gives details of how to restore back-ups, but I'd like to check to see whether they're actually being made nightly. su-ing to root I can access the second hard drive, but the only directory, Lost+Found is empty. Does this mean that cron.daily isn't running and how can I remedy this? I also have packages to update in the morning, which should also be run automatically by cron.daily, adding to my suspicions.
2. Has anyone attempted a native install of Qiime and its dependencies on Biolinux 6? http://qiime.sourceforge.net/install/install.html
I am having an issue getting various programs that are present to be recognised. I am editing .customrc in /etc/zsh/zshrc.d in order to set paths in zsh, but it doesn't seem to be working - is this the correct file to edit?
Thanks for your help
Mike Cox
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------------------------------
Message: 3
Date: Thu, 30 Sep 2010 08:46:24 +0100
From: "Tiwari, Bela" <btiwari at ceh.ac.uk>
Subject: Re: [Bio-Linux] Cron and Qiime
To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk>
Message-ID:
<1DCCED50D0696A498958BA6B254456E21F9DBB3002 at nerckwmb1.ad.nerc.ac.uk>
Content-Type: text/plain; charset="us-ascii"
Hi Mike,
Just addressing your second question for now:
>2. Has anyone attempted a native install of Qiime and its dependencies on Biolinux 6? http://qiime.sourceforge.net/install/install.html
> am having an issue getting various programs that are present to be recognised. I am editing .customrc in /etc/zsh/zshrc.d in order to set paths in zsh, but it doesn't seem to be working - is this the correct file to >edit?
/etc/zsh/zshrc.d/customrc is a reasonable file to edit, and as long as you're using a standard Bio-Linux user account, this file should be sourced.
For the Qiime specific part of the problem, maybe it's best to work using the NEBC helpdesk, and then, if the issues look like something that might benefit others, we can post a summary of steps taken to this list?
(Possibly we'll get closer towards a package solution if that looks feasable also.)
cheers,
Bela
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