From shou at ceh.ac.uk Mon Jan 5 11:01:54 2009 From: shou at ceh.ac.uk (Stewart Houten) Date: Mon, 5 Jan 2009 16:01:54 +0000 Subject: [Bio-Linux] USB media not automounted In-Reply-To: <495ACD55.1090904@abdn.ac.uk> References: <495ACD55.1090904@abdn.ac.uk> Message-ID: <20090105160154.GA30429@ivpcp068.nerc-oxford.ac.uk> Tony, On Dec 31, 2008, Tony Travis wrote: > Hello, > > I noticed that USB media were not being automounted after installing > Bio-Linux5 on my laptop from the Bio-Linux5 USB stick: I've traced the > problem to two incorrect entries in the /etc/fstab created during the > installation. It seems the installer thinks the USB stick is a CD/DVD > drive. A work-around is to comment out the two incorrect entries at the > end of /etc/fstab, and add a correct one for the real CD/DVD drive: > Thanks for this. I will add this to the troubleshooting section of the user guide and see if I can eliminate this behaviour on the image. Regards, Stewart From a.travis at abdn.ac.uk Sun Jan 11 19:35:36 2009 From: a.travis at abdn.ac.uk (Tony Travis) Date: Mon, 12 Jan 2009 00:35:36 +0000 Subject: [Bio-Linux] Bio-Linux5 local documentation Message-ID: <496A9058.6080000@abdn.ac.uk> Hello, Stewart. The local documentation for EMBOSS is broken. For example, the link for "abiview" is: file:///usr/local/bioinf/documentation/EMBOSS/doc/programs/html/abiview.html This file does not exist... A simple work-around is: cd /usr/local/bioinf/documentation ln -s /usr/local/bioinf/EMBOSS/EMBOSS-6.0.1/emboss/share/EMBOSS . I think that using 'file' URL's is bad, because they break when you access Bio-Linux documentation using an external web browser. I posted this 'fix' to make the documentation URL's relative to the webserver's document root under 'biobuntu' (Bio-Linux4 + Ubuntu 6.06) on the NBX: ----- cut here ----- #!/bin/sh # @(#)fix_bioinfo.sh 2007-09-28 A.J.Travis # # Fix file:/// URL's in Bio-Linux documentation # cd /var/www/bioinformatics/docs ln -s /usr/local/bioinf/documentation . for i in *.html; do ed $i < References: <496A9058.6080000@abdn.ac.uk> Message-ID: <20090116122640.GA19012@ivpcp068.nerc-oxford.ac.uk> Hello Tony, Thank you for the bug report. As you will have seen I have copied this email into our helpdesk as this issue relates to a bug in the Emboss package rather than more generally to Bio-Linux. I have fixed the bug in the package now so at the next update all machines should get fixed documentation. Since the files under emboss are installed by the package I would resist the temptation to modify things directly as it will likely cause conflicts with apt updates down the line. I'm sure you can work around this when it arises, Tony, but others may have more difficulty. FYI, our package convention is such that /usr/local/bioinf/EMBOSS/EMBOSS provides a link to EMBOSS-6.0.1 in the same directory and allows for future versions to point to the current installation. It might be worth noting for the future. Thanks also for pointing out the documentation URL issue. This doesn't cause an issue on a standard Bio-Linux setup but I can see that absolute URLs are redundant and how it causes a problem when trying to browse the docs across the network. Again the docs content is provided by a package, but the content is generated by a script that produces our live web version and the modified package content. When I have a little more time I will take another look at this. Regards, Stewart -- Dr Stewart Houten, Bio-Linux Developer NEBC, CEH, Mansfield Road, Oxford, OX1 3SR http://nebc.nox.ac.uk/ From Gary.Barker at bristol.ac.uk Wed Jan 21 09:01:43 2009 From: Gary.Barker at bristol.ac.uk (GLA Barker, School Biological Sciences) Date: Wed, 21 Jan 2009 14:01:43 +0000 Subject: [Bio-Linux] Biolinux virtual machine on a Mac using VMWARE Message-ID: <73F8DAA40D50041A6A367C66@gbmac.bio.bris.ac.uk> Hi there, Has anybody tried running biolinux as a virtual machine on an intel Mac under VMWARE fusion? I'd be grateful to know if its worth trying to set this up. Thanks, Gary ---------------------- Gary Barker PhD Bioinformatician School Biological Sciences University of Bristol, UK http://www.cerealsdb.uk.net From AdamsS5 at cardiff.ac.uk Wed Jan 21 09:39:33 2009 From: AdamsS5 at cardiff.ac.uk (Steffan Adams) Date: Wed, 21 Jan 2009 14:39:33 +0000 Subject: [Bio-Linux] Biolinux virtual machine on a Mac using VMWARE In-Reply-To: <73F8DAA40D50041A6A367C66@gbmac.bio.bris.ac.uk> References: <73F8DAA40D50041A6A367C66@gbmac.bio.bris.ac.uk> Message-ID: Gary We've got it running here as an image on vmware workstation for windows vista. I'm not familiar with fusion, but as long as it can create images using the biolinux iso file then I would imagine it will work. Regards Steff --- Steffan Adams Main Building, Park Place, Cardiff CF10 3AT Wales UK Tel: 02920874794 From: "GLA Barker, School Biological Sciences" To: Bio-Linux help and discussion Date: 21/01/2009 14:18 Subject: [Bio-Linux] Biolinux virtual machine on a Mac using VMWARE Hi there, Has anybody tried running biolinux as a virtual machine on an intel Mac under VMWARE fusion? I'd be grateful to know if its worth trying to set this up. Thanks, Gary ---------------------- Gary Barker PhD Bioinformatician School Biological Sciences University of Bristol, UK http://www.cerealsdb.uk.net _______________________________________________ Bio-Linux mailing list Bio-Linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux -------------- next part -------------- An HTML attachment was scrubbed... URL: From d.fulton at uea.ac.uk Wed Jan 21 10:00:20 2009 From: d.fulton at uea.ac.uk (Derek Fulton) Date: Wed, 21 Jan 2009 15:00:20 +0000 Subject: [Bio-Linux] Biolinux virtual machine on a Mac using VMWARE In-Reply-To: <73F8DAA40D50041A6A367C66@gbmac.bio.bris.ac.uk> References: <73F8DAA40D50041A6A367C66@gbmac.bio.bris.ac.uk> Message-ID: HI Gary, Have you Bootcamp & OSX leopard? Regards Derek At 14:01 21/01/2009, you wrote: >Hi there, >Has anybody tried running biolinux as a virtual machine on an intel Mac >under VMWARE fusion? I'd be grateful to know if its worth trying to set >this up. > >Thanks, >Gary > > >---------------------- >Gary Barker PhD >Bioinformatician >School Biological Sciences >University of Bristol, UK >http://www.cerealsdb.uk.net > >_______________________________________________ >Bio-Linux mailing list >Bio-Linux at envgen.nox.ac.uk >http://envgen.nox.ac.uk/mailman/listinfo/bio-linux ----------------------------------------- D.Fulton I.T. Manager School of Biological Sciences University of East Anglia Norwich NR4 7TJ Norfolk England UK Tel: 01603 592188 (direct line) Fax: 01603 592250 e-mail: D.Fulton at uea.ac.uk Internal computing problems to bio.help at uea.ac.uk WWW Server URL: http://www.uea.ac.uk/bio --------------------OOO------------------ From Gary.Barker at bristol.ac.uk Wed Jan 21 10:05:28 2009 From: Gary.Barker at bristol.ac.uk (GLA Barker, School Biological Sciences) Date: Wed, 21 Jan 2009 15:05:28 +0000 Subject: [Bio-Linux] Biolinux virtual machine on a Mac using VMWARE In-Reply-To: References: <73F8DAA40D50041A6A367C66@gbmac.bio.bris.ac.uk> Message-ID: <99F36F537B266F0BA2AFD347@gbmac.bio.bris.ac.uk> Yes, I've got Leopard and bootcamp with a ~ 30 Gig WinXP partition. Cheers, Gary --On Wednesday, January 21, 2009 15:00 +0000 Derek Fulton wrote: > HI Gary, > Have you Bootcamp & OSX leopard? > Regards > Derek > > > At 14:01 21/01/2009, you wrote: >> Hi there, >> Has anybody tried running biolinux as a virtual machine on an intel Mac >> under VMWARE fusion? I'd be grateful to know if its worth trying to set >> this up. >> >> Thanks, >> Gary >> >> >> ---------------------- >> Gary Barker PhD >> Bioinformatician >> School Biological Sciences >> University of Bristol, UK >> http://www.cerealsdb.uk.net >> >> _______________________________________________ >> Bio-Linux mailing list >> Bio-Linux at envgen.nox.ac.uk >> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > > ----------------------------------------- > D.Fulton > I.T. Manager > School of Biological Sciences > University of East Anglia > Norwich NR4 7TJ > Norfolk > England UK > Tel: 01603 592188 (direct line) > Fax: 01603 592250 > e-mail: D.Fulton at uea.ac.uk > Internal computing problems to bio.help at uea.ac.uk > WWW Server URL: http://www.uea.ac.uk/bio > --------------------OOO------------------ > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux ---------------------- Gary Barker PhD Bioinformatician School Biological Sciences University of Bristol, UK http://www.cerealsdb.uk.net From pasko at biol.uni.wroc.pl Wed Jan 21 12:22:50 2009 From: pasko at biol.uni.wroc.pl (=?ISO-8859-2?Q?=A3ukasz_Pa=B6ko?=) Date: Wed, 21 Jan 2009 18:22:50 +0100 Subject: [Bio-Linux] Biolinux virtual machine on a Mac using VMWARE In-Reply-To: <73F8DAA40D50041A6A367C66@gbmac.bio.bris.ac.uk> References: <73F8DAA40D50041A6A367C66@gbmac.bio.bris.ac.uk> Message-ID: <3C46142F-7C47-4384-AE40-FEA4CF907639@biol.uni.wroc.pl> Hi, BioLinux works great as a virtual machine under VMWARE FUSION 2.0 and MacOSX 10.5.6. Small problems (but maybe only computer-specific) are with installing VMWare Tools (enhanced video drives etc.) Best Regards Lukasz ~~~ Lukasz Pasko PhD Department of Vertebrate Zoology and Laboratory of DNA Analysis Institute of Zoology University of Wroclaw Sienkiewicz street 21 50-335 Wroclaw Poland Wiadomo?? napisana w dniu 2009-01-21, o godz. 15:01, przez GLA Barker, School Biological Sciences: > Hi there, > Has anybody tried running biolinux as a virtual machine on an intel > Mac > under VMWARE fusion? I'd be grateful to know if its worth trying to > set > this up. > > Thanks, > Gary > > > ---------------------- > Gary Barker PhD > Bioinformatician > School Biological Sciences > University of Bristol, UK > http://www.cerealsdb.uk.net > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From a.travis at abdn.ac.uk Wed Jan 21 17:24:28 2009 From: a.travis at abdn.ac.uk (Travis, Tony) Date: Wed, 21 Jan 2009 22:24:28 +0000 Subject: [Bio-Linux] Bio-Linux on the Ubuntu community wiki Message-ID: I've posted a link to Bio-Linux project on the Ubuntu community wiki: https://help.ubuntu.com/community/UbuntuScience/Biology#Bio-Linux 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 The University of Aberdeen is a charity registered in Scotland, No SC013683. From a.travis at abdn.ac.uk Wed Jan 28 10:26:09 2009 From: a.travis at abdn.ac.uk (Tony Travis) Date: Wed, 28 Jan 2009 15:26:09 +0000 Subject: [Bio-Linux] Bio-Linux 5.0 security Message-ID: <49807911.6020709@abdn.ac.uk> Hello, I've just installed Bio-Linux 5.0.2 on one of our NuGO servers (nbx1). I'm pleased to see that "openssh-server" is pre-installed in Bio-Linux, but I think it might be wise to install "fail2ban" as well, to defend against 'brute-force' attacks from the Internet via SSH. I've done this on "nbx1", and I've also installed "linux-server", which depends on the latest version of the Ubuntu Linux kernel for 'server' equipment. The 'server' kernel supports PAE (Physical Address extension), which allows 32-bit systems to use >4GB RAM. Any one 32-bit process can't access more than 4GB RAM, but several 32-bit processes can use > 4GB in total. Thanks for all the work you've put into the latest Bio-Linux release! Bye, 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 From tbooth at ceh.ac.uk Wed Jan 28 10:46:11 2009 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 28 Jan 2009 15:46:11 +0000 Subject: [Bio-Linux] Bio-Linux 5.0 security In-Reply-To: <49807911.6020709@abdn.ac.uk> References: <49807911.6020709@abdn.ac.uk> Message-ID: <1233157571.8245.31.camel@barsukas> Hi Tony, Useful advice, but a word of warning on fail2ban - I've known it to block legitimate hosts, including even localhost! It seems that NX, which a lot of people use for remote access, did not play nicely with fail2ban in that case. If you have a small number of users on a machine (eg. if it is just your personal workstation) I would ensure that membership of the ssh group is kept to a minimum, use hard-to-crack passwords (http://www.dowling.edu/mydowling/tech/good-passwords.html) and consider moving from password-based login to key-based login. Key-based login takes a little bit of work to set up but is immune to current 'brute-force' attacks and can actually save you time typing passwords. If anyone on this list is interested in knowing more then let me know and I'll post some details. Cheers, TIM On Wed, 2009-01-28 at 15:26 +0000, Tony Travis wrote: > Hello, > > I've just installed Bio-Linux 5.0.2 on one of our NuGO servers (nbx1). > > I'm pleased to see that "openssh-server" is pre-installed in Bio-Linux, > but I think it might be wise to install "fail2ban" as well, to defend > against 'brute-force' attacks from the Internet via SSH. I've done this > on "nbx1", and I've also installed "linux-server", which depends on the > latest version of the Ubuntu Linux kernel for 'server' equipment. The > 'server' kernel supports PAE (Physical Address extension), which allows > 32-bit systems to use >4GB RAM. Any one 32-bit process can't access more > than 4GB RAM, but several 32-bit processes can use > 4GB in total. > > Thanks for all the work you've put into the latest Bio-Linux release! > > Bye, > > 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 > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NERC Environmental Bioinformatics Centre at CEH Oxford +44 1865 281 975 From a.travis at abdn.ac.uk Wed Jan 28 11:46:13 2009 From: a.travis at abdn.ac.uk (Tony Travis) Date: Wed, 28 Jan 2009 16:46:13 +0000 Subject: [Bio-Linux] Bio-Linux 5.0 security In-Reply-To: <1233157571.8245.31.camel@barsukas> References: <49807911.6020709@abdn.ac.uk> <1233157571.8245.31.camel@barsukas> Message-ID: <49808BD5.3070000@abdn.ac.uk> Tim Booth wrote: > Hi Tony, > > Useful advice, but a word of warning on fail2ban - I've known it to > block legitimate hosts, including even localhost! It seems that NX, > which a lot of people use for remote access, did not play nicely with > fail2ban in that case. Hello, Tim. We've been using "fail2ban" with NX on our Beowulf at RINH and the NBX network without any problems. The default configuration that I'm using un-bans hosts after ten minutes anyway. Maybe the problem is only when you use the Nomachine proprietary 'free' NX server ;-) Without "fail2ban", our systems are more vulnerable to this sort of attack from the Internet. I wrote an admin script called 'incoming' (attached) to monitor login activity. This gives me more information about where the failed login attempts are coming from than "faillog". > If you have a small number of users on a machine (eg. if it is just your > personal workstation) I would ensure that membership of the ssh group is > kept to a minimum, use hard-to-crack passwords > (http://www.dowling.edu/mydowling/tech/good-passwords.html) and consider > moving from password-based login to key-based login. Yes. you're right about "hard-to-crack passwords", but theft of keys is almost as much of a risk as theft of passwords :-( > Key-based login takes a little bit of work to set up but is immune to > current 'brute-force' attacks and can actually save you time typing > passwords. If anyone on this list is interested in knowing more then > let me know and I'll post some details. Brute-force attacks become denial of service attacks if you don't use fail2ban because you allow an attacker to continue attempting to login. If you use fail2ban, the attacker doesn't even get a response to their TCP/IP packets because fail2ban modifies the kernel IPTABLES to drop any packets from the suspect host IP address. Key-based login does not do anything to prevent continued (futile) attacks... We already use SSH key-based logins, and LDAP certificates on the NBX. However, I am interested in any jungle tips that you can give us about how to defend Bio-Linux systems. Bye, 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 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: incoming URL: From A.J.Pemberton at bham.ac.uk Wed Jan 28 12:25:32 2009 From: A.J.Pemberton at bham.ac.uk (Anthony Pemberton) Date: Wed, 28 Jan 2009 17:25:32 +0000 Subject: [Bio-Linux] Bio-Linux 5.0 security In-Reply-To: <1233157571.8245.31.camel@barsukas> References: <49807911.6020709@abdn.ac.uk> <1233157571.8245.31.camel@barsukas> Message-ID: Dear All, Another approach is to simply secure the firewall further by only allowing certain machines or subnets to access sshd. This can be done fairly simply with iptables by adding the -s option to the sshd line in the iptables config. Also by using tcp_wrappers to also limit access. Obviously this depends on how much the admin wants to limit access, Regards, Tony Pemberton > -----Original Message----- > From: bio-linux-bounces at envgen.nerc-oxford.ac.uk [mailto:bio-linux- > bounces at envgen.nerc-oxford.ac.uk] On Behalf Of Tim Booth > Sent: 28 January 2009 15:46 > To: Bio-Linux help and discussion > Subject: Re: [Bio-Linux] Bio-Linux 5.0 security > > Hi Tony, > > Useful advice, but a word of warning on fail2ban - I've known it to > block legitimate hosts, including even localhost! It seems that NX, > which a lot of people use for remote access, did not play nicely with > fail2ban in that case. > > If you have a small number of users on a machine (eg. if it is just > your > personal workstation) I would ensure that membership of the ssh group > is > kept to a minimum, use hard-to-crack passwords > (http://www.dowling.edu/mydowling/tech/good-passwords.html) and > consider > moving from password-based login to key-based login. > > Key-based login takes a little bit of work to set up but is immune to > current 'brute-force' attacks and can actually save you time typing > passwords. If anyone on this list is interested in knowing more then > let me know and I'll post some details. > > Cheers, > > TIM > > On Wed, 2009-01-28 at 15:26 +0000, Tony Travis wrote: > > Hello, > > > > I've just installed Bio-Linux 5.0.2 on one of our NuGO servers > (nbx1). > > > > I'm pleased to see that "openssh-server" is pre-installed in Bio- > Linux, > > but I think it might be wise to install "fail2ban" as well, to defend > > against 'brute-force' attacks from the Internet via SSH. I've done > this > > on "nbx1", and I've also installed "linux-server", which depends on > the > > latest version of the Ubuntu Linux kernel for 'server' equipment. The > > 'server' kernel supports PAE (Physical Address extension), which > allows > > 32-bit systems to use >4GB RAM. Any one 32-bit process can't access > more > > than 4GB RAM, but several 32-bit processes can use > 4GB in total. > > > > Thanks for all the work you've put into the latest Bio-Linux release! > > > > Bye, > > > > 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 > > > > _______________________________________________ > > Bio-Linux mailing list > > Bio-Linux at envgen.nox.ac.uk > > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux > -- > Tim Booth > NERC Environmental Bioinformatics Centre > at CEH Oxford > +44 1865 281 975 > > > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux