From tbooth at ceh.ac.uk Wed Jun 2 06:51:27 2010 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 02 Jun 2010 11:51:27 +0100 Subject: [Bio-linux-dev] bio-linux-backups In-Reply-To: <4BFB1AC0.8030608@abdn.ac.uk> References: <4BF010FD.2020208@abdn.ac.uk> <1274085154.15465.224.camel@barsukas> <4BF3F431.7050101@abdn.ac.uk> <1274718955.23154.32.camel@barsukas> <4BFB1AC0.8030608@abdn.ac.uk> Message-ID: <1275475887.5036.50.camel@barsukas> Hi, I've rolled a new bio-linux-backups package based on Tony's patch. This may be over-conservative of me but I thought that anyone already using the backups script should keep the old behaviour by default. Therefore I've made the package so that if you are upgrading from an old (version 0.2) package and no /etc/default/backup configuration file is found, a configuration file will be added containing: MODE=basic For fresh installations (eg. BL6) and future upgrades the config will be untouched and the default behaviour is to use ETOH. I've also added a script that summarises some info about the backup status - /usr/sbin/bio-linux-backup-info. Attached is the new package if you want a sneak preview - it's not in the repo yet. Cheers, TIM -- 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. -------------- next part -------------- A non-text attachment was scrubbed... Name: bio-linux-backups_0.3-3_all.deb Type: application/x-deb Size: 7178 bytes Desc: not available URL: From tbooth at ceh.ac.uk Mon Jun 7 04:53:03 2010 From: tbooth at ceh.ac.uk (Tim Booth) Date: Mon, 07 Jun 2010 09:53:03 +0100 Subject: [Bio-linux-dev] Bio-Linux 6 release - thanks to testers Message-ID: <1275900783.22487.61.camel@barsukas> Dear All, As you would have seen in the announcement yesterday (http://nebclists.nerc.ac.uk/pipermail/bio-linux-announce/2010-June/000007.html), Bio-Linux 6.0 was released on schedule. Many thanks to all the people on this list who helped test beta versions of the system and provided feedback. Please continue to send any questions or suggestions to the helpdesk address - in many cases we will be able to fix issues with package updates even if there is a problem with the actual image. For those running B1 or B2, you do not need to re-install but be aware of the following issues that will not be fixed by simply upgrading packages: 1. Many R libraries are missing off the system. If you wish to use these, they need to be installed manually - full instructions are here: http://nebc.nerc.ac.uk/tools/bioinformatics-docs/other-bioinf/r-and-bioconductor/?searchterm=cran 2. You may want to remove firestarter and install gufw as this is now the default firewall configurator. 3. If you use the default automated nightly backups, you should update the package and run bio-linux-backup-info to check that the settings are correct (see /etc/default/backup). 4. You can install the bio-linux-tutorials, bio-linux-arb and bio-linux-genquery packages which are not on earlier images 5. You can install maq, velvet and ssake packages which are not on the earlier images 6. You can add the EB-Eye search to Firefox by going to: http://www.ebi.ac.uk/inc/help/search_help.html#addebeye 7. You should setup logcheck as detailed in the user guide, or else turn it off to stop daily logcheck mails accumulating in /var/mail/spool. 8. The branding has changed slightly in the final release - startup and shutdown logos, login manager and default wallpaper are new. This is just cosmetic. 9. FreeNX server may not work on all beta versions - this can normally be fixed by doing 'sudo dpkg-reconfigure -pcritical freenx-server'. 10. Beta 1 did not have the automatic upgrades or update notification set up as described in the user guide. You will need to periodically run the update manager to get new bioinformatics packages (you would need to do this anyway to get Ubuntu updates). 11. There was an issue with 'umask' setting on B1 - on an installed system if you type 'sudo -i' (give password if asked) then 'umask' you should get 0022. If you see 0077 then you need to run 'sudo visudo' and add the following line at the end of the file: Defaults umask_override I hope you enjoy using Bio-Linux 6. Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre at CEH Wallingford +44 1491 69 2705 -- 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 joachim.jacob at vib.be Wed Jun 9 09:35:53 2010 From: joachim.jacob at vib.be (Joachim Jacob) Date: Wed, 09 Jun 2010 15:35:53 +0200 Subject: [Bio-linux-dev] Biolinux 6 Torrent Message-ID: <4C0F98B9.1080501@vib.be> Dear all, Now there is a torrent for Biolinux 6 on www.biotorrents.net, see http://www.biotorrents.net/details.php?id=90 Cheers, Joachim. -- BITS logo * Joachim Jacob, PhD. * Bioinformatics Trainer BITS - www.bits.vib.be VIB - www.vib.be VIB headquarters, Rijvisschestraat 120, BE-9052 Gent, Belgium (see map ) Tel.: +32 9 244 66 11 Fax.: +32 9 244 66 10 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: logo-default.jpg Type: image/jpeg Size: 14628 bytes Desc: not available URL: From tbooth at ceh.ac.uk Wed Jun 9 09:50:53 2010 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 09 Jun 2010 14:50:53 +0100 Subject: [Bio-linux-dev] Biolinux 6 Torrent In-Reply-To: <4C0F98B9.1080501@vib.be> References: <4C0F98B9.1080501@vib.be> Message-ID: <1276091453.22487.160.camel@barsukas> Hi Joachim, Thanks for uploading this. There are already people asking for a torrent link so i will forward it on. I guess it's too late now, but I should have asked you to upload the file as bio-linux-6.0.22.iso. There's going to be a 6.0.23 very shortly as I have fixed a few glitches over the last week (nothing serious). Cheers, TIM On Wed, 2010-06-09 at 14:35 +0100, Joachim Jacob wrote: > Dear all, > > Now there is a torrent for Biolinux 6 on www.biotorrents.net, see > http://www.biotorrents.net/details.php?id=90 > > Cheers, > Joachim. > -- > > BITS logo > > Joachim Jacob, PhD. > Bioinformatics Trainer > BITS - www.bits.vib.be > VIB - www.vib.be > VIB headquarters, Rijvisschestraat 120, BE-9052 Gent, Belgium (see > map) > Tel.: +32 9 244 66 11 Fax.: +32 9 244 66 10 > > -- Tim Booth NERC Environmental Bioinformatics Centre at CEH Wallingford +44 1491 69 2705 -- 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 a.travis at abdn.ac.uk Wed Jun 9 10:34:07 2010 From: a.travis at abdn.ac.uk (Tony Travis) Date: Wed, 09 Jun 2010 15:34:07 +0100 Subject: [Bio-linux-dev] Biolinux 6 Torrent In-Reply-To: <1276091453.22487.160.camel@barsukas> References: <4C0F98B9.1080501@vib.be> <1276091453.22487.160.camel@barsukas> Message-ID: <4C0FA65F.90404@abdn.ac.uk> On 09/06/10 14:50, Tim Booth wrote: > Hi Joachim, > > Thanks for uploading this. There are already people asking for a > torrent link so i will forward it on. > > I guess it's too late now, but I should have asked you to upload the > file as bio-linux-6.0.22.iso. There's going to be a 6.0.23 very shortly > as I have fixed a few glitches over the last week (nothing serious). Hello, Tim. Minor bug: Your backup info script gets confused by any sub-directories, including 'lost+found', in /backups: Bye, Tony. > manager at nbx1[/manager] sudo /usr/sbin/bio-linux-backup-info [ 3:29PM] > [sudo] password for manager: > Configuration loaded from /etc/default/backup. > Backup mode: etoh > Destination: /backups > What to backup: / /home > Compression: z > > Mounting /backups for inspection... > > Backups found for lost+found. > 32 total files found = 272G. > Latest file is dated Wed Jun 9 07:56:00 BST 2010 (md0.bak.8). > Backup area on /dev/sde3 (417G) is 69% full with 125G space available. > > For a full restoration, restore in this order: > Oops - problem processing lost+found. > md0.bak.0 > md0.bak.1 > md0.bak.5 > md0.bak.8 > > Oops - problem processing old. > sda1.bak.0 > sda1.bak.1 > sda1.bak.2 > > sde1.bak.0 > sde1.bak.1 > sde1.bak.5 > sde1.bak.8 > > Unmounting /backups... DONE. -- 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 From joachim.jacob at vib.be Thu Jun 10 04:53:48 2010 From: joachim.jacob at vib.be (Joachim Jacob) Date: Thu, 10 Jun 2010 10:53:48 +0200 Subject: [Bio-linux-dev] Bio-Linux-dev Torrent In-Reply-To: References: Message-ID: <4C10A81C.7050908@vib.be> Hi Tim, Okay, you're right. When the new version is ready, I will make a new torrent with a more specific name. Cheers, Joachim On 09/06/10 16:34, bio-linux-dev-request at nebclists.nerc.ac.uk wrote: > Send Bio-Linux-dev mailing list submissions to > bio-linux-dev at nebclists.nerc.ac.uk > > To subscribe or unsubscribe via the World Wide Web, visit > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev > or, via email, send a message with subject or body 'help' to > bio-linux-dev-request at nebclists.nerc.ac.uk > > You can reach the person managing the list at > bio-linux-dev-owner at nebclists.nerc.ac.uk > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bio-Linux-dev digest..." > > > Today's Topics: > > 1. Biolinux 6 Torrent (Joachim Jacob) > 2. Re: Biolinux 6 Torrent (Tim Booth) > 3. Re: Biolinux 6 Torrent (Tony Travis) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 09 Jun 2010 15:35:53 +0200 > From: Joachim Jacob > Subject: [Bio-linux-dev] Biolinux 6 Torrent > To: bio-linux-dev at nebclists.nerc.ac.uk > Message-ID: <4C0F98B9.1080501 at vib.be> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > Now there is a torrent for Biolinux 6 on www.biotorrents.net, see > http://www.biotorrents.net/details.php?id=90 > > Cheers, > Joachim. > -- BITS logo * Joachim Jacob, PhD. * Bioinformatics Trainer BITS - www.bits.vib.be VIB - www.vib.be VIB headquarters, Rijvisschestraat 120, BE-9052 Gent, Belgium (see map ) Tel.: +32 9 244 66 11 Fax.: +32 9 244 66 10 -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: logo-default.jpg Type: image/jpeg Size: 14628 bytes Desc: not available URL: From tbooth at ceh.ac.uk Tue Jun 15 12:41:16 2010 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 15 Jun 2010 17:41:16 +0100 Subject: [Bio-linux-dev] Bio-Linux 6.0.23 Message-ID: <1276620076.9737.87.camel@barsukas> Hi Joachim, There is a new point release of Bio-Linux on the site: http://nebc.nerc.ac.uk/downloads/bio-linux-6.0.23.iso I can see there were 8 downloads of the last image so it looks like some people are appreciating the torrent, if you have time to put the new one up. There's no crucial changes from 6.0.22, just several of our packages have been tweaked and updated so this release carries the fixed versions. Also some requisites have been added to make Rcmdr work properly. Additionally the Priam package is not on there by default, saving a little space. I don't anticipate a further update for several weeks at least. This is the version we're sending out to USB requestors. Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre at CEH Wallingford +44 1491 69 2705 -- 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.