From michael.cox1 at imperial.ac.uk Wed Sep 29 10:40:36 2010 From: michael.cox1 at imperial.ac.uk (Cox, Michael J) Date: Wed, 29 Sep 2010 15:40:36 +0100 Subject: [Bio-Linux] Cron and Qiime Message-ID: 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 From A.J.Pemberton at bham.ac.uk Wed Sep 29 11:23:26 2010 From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton) Date: Wed, 29 Sep 2010 16:23:26 +0100 Subject: [Bio-Linux] Cron and Qiime In-Reply-To: References: Message-ID: <3A5B0BBDAF00724AB5F10155650102300216806BC4@LESMBX1.adf.bham.ac.uk> 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 _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux From btiwari at ceh.ac.uk Thu Sep 30 03:46:24 2010 From: btiwari at ceh.ac.uk (Tiwari, Bela) Date: Thu, 30 Sep 2010 08:46:24 +0100 Subject: [Bio-Linux] Cron and Qiime In-Reply-To: References: Message-ID: <1DCCED50D0696A498958BA6B254456E21F9DBB3002@nerckwmb1.ad.nerc.ac.uk> 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 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. From michael.cox1 at imperial.ac.uk Thu Sep 30 08:03:16 2010 From: michael.cox1 at imperial.ac.uk (Cox, Michael J) Date: Thu, 30 Sep 2010 13:03:16 +0100 Subject: [Bio-Linux] Cron and Qiime Message-ID: 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 ________________________________________ From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of bio-linux-request at nebclists.nerc.ac.uk [bio-linux-request at nebclists.nerc.ac.uk] Sent: Thursday, September 30, 2010 12:00 PM To: bio-linux at nebclists.nerc.ac.uk Subject: Bio-Linux Digest, Vol 35, Issue 1 Send Bio-Linux mailing list submissions to bio-linux at nebclists.nerc.ac.uk To subscribe or unsubscribe via the World Wide Web, visit http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux or, via email, send a message with subject or body 'help' to bio-linux-request at nebclists.nerc.ac.uk You can reach the person managing the list at bio-linux-owner at nebclists.nerc.ac.uk When replying, please edit your Subject line so it is more specific than "Re: Contents of Bio-Linux digest..." 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" Subject: [Bio-Linux] Cron and Qiime To: "bio-linux at nebclists.nerc.ac.uk" Message-ID: 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 Subject: Re: [Bio-Linux] Cron and Qiime To: Bio-Linux help and discussion 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 _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux ------------------------------ Message: 3 Date: Thu, 30 Sep 2010 08:46:24 +0100 From: "Tiwari, Bela" Subject: Re: [Bio-Linux] Cron and Qiime To: Bio-Linux help and discussion 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 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. ------------------------------ _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux End of Bio-Linux Digest, Vol 35, Issue 1 **************************************** From A.J.Pemberton at bham.ac.uk Thu Sep 30 10:12:31 2010 From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton) Date: Thu, 30 Sep 2010 15:12:31 +0100 Subject: [Bio-Linux] Cron and Qiime In-Reply-To: References: Message-ID: <3A5B0BBDAF00724AB5F10155650102300216806C1D@LESMBX1.adf.bham.ac.uk> 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, Regards, Tony P. -----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: 30 September 2010 13:03 To: bio-linux at nebclists.nerc.ac.uk Subject: Re: [Bio-Linux] Cron and Qiime 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 ________________________________________ From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of bio-linux-request at nebclists.nerc.ac.uk [bio-linux-request at nebclists.nerc.ac.uk] Sent: Thursday, September 30, 2010 12:00 PM To: bio-linux at nebclists.nerc.ac.uk Subject: Bio-Linux Digest, Vol 35, Issue 1 Send Bio-Linux mailing list submissions to bio-linux at nebclists.nerc.ac.uk To subscribe or unsubscribe via the World Wide Web, visit http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux or, via email, send a message with subject or body 'help' to bio-linux-request at nebclists.nerc.ac.uk You can reach the person managing the list at bio-linux-owner at nebclists.nerc.ac.uk When replying, please edit your Subject line so it is more specific than "Re: Contents of Bio-Linux digest..." 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" Subject: [Bio-Linux] Cron and Qiime To: "bio-linux at nebclists.nerc.ac.uk" Message-ID: 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 Subject: Re: [Bio-Linux] Cron and Qiime To: Bio-Linux help and discussion 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 _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux ------------------------------ Message: 3 Date: Thu, 30 Sep 2010 08:46:24 +0100 From: "Tiwari, Bela" Subject: Re: [Bio-Linux] Cron and Qiime To: Bio-Linux help and discussion 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 -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. ------------------------------ _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux End of Bio-Linux Digest, Vol 35, Issue 1 **************************************** _______________________________________________ Bio-Linux mailing list Bio-Linux at nebclists.nerc.ac.uk http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux