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</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoPlainText>Please see the following messages.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Thanks in advance.<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Stephen P. Molnar, Ph.D. Life is a fuzzy set<o:p></o:p></p><p class=MsoPlainText>Foundation for Chemistry Stochastic and multivariate<o:p></o:p></p><p class=MsoPlainText><a href="http://www.FoundationForChemistry.com">www.FoundationForChemistry.com</a><o:p></o:p></p><p class=MsoPlainText>(614)312-7528 (c)<o:p></o:p></p><p class=MsoPlainText>Skype: smolnar1<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>-----Original Message-----<o:p></o:p></p><p class=MsoPlainText>From: Tim Booth [<a href="mailto:tbooth@ceh.ac.uk">mailto:tbooth@ceh.ac.uk</a>]<o:p></o:p></p><p class=MsoPlainText>Sent: Friday, August 01, 2014 9:40 AM<o:p></o:p></p><p class=MsoPlainText>To: Stephen P. Molnar<o:p></o:p></p><p class=MsoPlainText>Subject: Re: [Bio-linux-announce] Bio-Linux 8 now available<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Hi Stephen,<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Glad you sorted out the shell. <o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>I'm sorry, but I can't say what might be up with the keyboard and I'm not going to start experimenting with XFCE right now as I have other priorities. You may well have more luck on the discussion mailing list:<o:p></o:p></p><p class=MsoPlainText><a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux</a><o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Cheers,<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>TIM<o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>On Fri, 2014-08-01 at 11:59 +0100, Stephen P. Molnar wrote:<o:p></o:p></p><p class=MsoPlainText>> Thanks for the reply. As it turns out that was a red-faced forehead <o:p></o:p></p><p class=MsoPlainText>> slapping problem. After dispatching my note I realized that the shell <o:p></o:p></p><p class=MsoPlainText>> was zsh.<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> Thanks to your reply I have successfully changed the default shell to <o:p></o:p></p><p class=MsoPlainText>> bash.<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> There is, however anew problem, also a head scratcher for me. As I <o:p></o:p></p><p class=MsoPlainText>> don't like the Gnome shell and had become unenchanted with KDE, my <o:p></o:p></p><p class=MsoPlainText>> desktop of choice on my linux machines is XFCE, with Xfe as the file <o:p></o:p></p><p class=MsoPlainText>> manager of choice. I find that the keyboard doesn't seem to be <o:p></o:p></p><p class=MsoPlainText>> recognized by the xfwrite editor. On the other hand, nedit works as it <o:p></o:p></p><p class=MsoPlainText>> should.<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> Your input about this problem would be much appreciated.<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> Thanks in advance.<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> Stephen P. Molnar, Ph.D. Life is a fuzzy set<o:p></o:p></p><p class=MsoPlainText>> Foundation for Chemistry Stochastic and multivariate<o:p></o:p></p><p class=MsoPlainText>> <a href="http://www.FoundationForChemistry.com">www.FoundationForChemistry.com</a><o:p></o:p></p><p class=MsoPlainText>> (614)312-7528 (c)<o:p></o:p></p><p class=MsoPlainText>> Skype: smolnar1<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> -----Original Message-----<o:p></o:p></p><p class=MsoPlainText>> From: Tim Booth [<a href="mailto:tbooth@ceh.ac.uk">mailto:tbooth@ceh.ac.uk</a>]<o:p></o:p></p><p class=MsoPlainText>> Sent: Friday, August 01, 2014 5:05 AM<o:p></o:p></p><p class=MsoPlainText>> To: Stephen P. Molnar<o:p></o:p></p><p class=MsoPlainText>> Subject: Re: [Bio-linux-announce] Bio-Linux 8 now available<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> Hi Stephen,<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> Nothing so mysterious here. The default shell on Bio-Linux is ZSH, so if you are a BASH fan you'll want to do:<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> chsh -s /bin/bash<o:p></o:p></p><p class=MsoPlainText>> exec bash -l<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> We do already have both L and ll aliased to that command, but not "l" <o:p></o:p></p><p class=MsoPlainText>> :-)<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> Cheers,<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> TIM<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> On Thu, 2014-07-31 at 20:16 +0100, Stephen P. Molnar wrote:<o:p></o:p></p><p class=MsoPlainText>> > I have encountered a rather strange problem with the new BioLinux v<o:p></o:p></p><p class=MsoPlainText>> > 8 latest.<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > I installed the distribution in a VMware Player without any problems <o:p></o:p></p><p class=MsoPlainText>> > or error messages. In fact, I have a Debian v-7.6.0 distribution <o:p></o:p></p><p class=MsoPlainText>> > running in the same VMware device. Consequently, I have confidence <o:p></o:p></p><p class=MsoPlainText>> > in the virtual computer and my laptop on which it is running.<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > I edited .bashrc to include the line alias l='ls -l --color'<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > When I source the edited .bashrc file I get the following:<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > computation@inga[computation] source .bashrc [<o:p></o:p></p><p class=MsoPlainText>> > 2:57PM]<o:p></o:p></p><p class=MsoPlainText>> > .bashrc:16: command not found: shopt<o:p></o:p></p><p class=MsoPlainText>> > .bashrc:24: command not found: shopt<o:p></o:p></p><p class=MsoPlainText>> > .bashrc:108: command not found: shopt<o:p></o:p></p><p class=MsoPlainText>> > /usr/share/bash-completion/bash_completion:35: parse error near `]]'<o:p></o:p></p><p class=MsoPlainText>> > \[\e]0;\u@\h: \w\a\]${debian_chroot:+($debian_chroot)}\u@\h:\w\$ [<o:p></o:p></p><p class=MsoPlainText>> > 2:57PM]<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > The problem seems to be that shopt is missing!<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > Please advise.<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > Thanks in advance.<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > Stephen P. Molnar, Ph.D. Life is a fuzzy<o:p></o:p></p><p class=MsoPlainText>> > set<o:p></o:p></p><p class=MsoPlainText>> > Foundation for Chemistry Stochastic and<o:p></o:p></p><p class=MsoPlainText>> > multivariate<o:p></o:p></p><p class=MsoPlainText>> > <a href="http://www.FoundationForChemistry.com">www.FoundationForChemistry.com</a><o:p></o:p></p><p class=MsoPlainText>> > (614)312-7528 (c)<o:p></o:p></p><p class=MsoPlainText>> > Skype: smolnar1<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > -----Original Message-----<o:p></o:p></p><p class=MsoPlainText>> > From: Tim Booth [<a href="mailto:tbooth@ceh.ac.uk">mailto:tbooth@ceh.ac.uk</a>]<o:p></o:p></p><p class=MsoPlainText>> > Sent: Wednesday, July 30, 2014 11:55 AM<o:p></o:p></p><p class=MsoPlainText>> > To: <a href="mailto:bio-linux-announce@nebclists.nerc.ac.uk">bio-linux-announce@nebclists.nerc.ac.uk</a>; Bio-Linux mailing list<o:p></o:p></p><p class=MsoPlainText>> > Subject: [Bio-linux-announce] Bio-Linux 8 now available<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > Dear All,<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > The Bio-Linux system gets a major new release every two years <o:p></o:p></p><p class=MsoPlainText>> > following the regular Ubuntu "LTS" releases. Since Ubuntu 14.04 LTS <o:p></o:p></p><p class=MsoPlainText>> > came out in April I've been working with help from the Bio-Linux <o:p></o:p></p><p class=MsoPlainText>> > community to make Bio-Linux 8 and it is now ready and available via the new website.<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > <a href="http://environmentalomics.org/bio-linux/">http://environmentalomics.org/bio-linux/</a><o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > Upgrades from Bio-Linux 7 to 8 do not require re-installation. I <o:p></o:p></p><p class=MsoPlainText>> > encourage you all to upgrade soon, as new bioinformatics packages <o:p></o:p></p><p class=MsoPlainText>> > will no longer be provided for Bio-Linux 7. See the "Installation"<o:p></o:p></p><p class=MsoPlainText>> > section for instructions on upgrading your BL7 machine.<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > The new Ubuntu 14.04 base system brings many benefits such as <o:p></o:p></p><p class=MsoPlainText>> > increased hardware compatibility and new office and multimedia <o:p></o:p></p><p class=MsoPlainText>> > software, but Bio-Linux itself also has many improvements and new/updated packages.<o:p></o:p></p><p class=MsoPlainText>> > Also for the first time there is a version in OVA format for <o:p></o:p></p><p class=MsoPlainText>> > VirtualBox/VMWare users, and this version will be updated whenever <o:p></o:p></p><p class=MsoPlainText>> > new ISO files are released. See the "What's New" and "Software List"<o:p></o:p></p><p class=MsoPlainText>> > pages on the website for details.<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > As ever, please report problems and feedback to <o:p></o:p></p><p class=MsoPlainText>> > <a href="mailto:helpdesk@nebc.nerc.ac.uk">helpdesk@nebc.nerc.ac.uk</a>. I can't promise to fix everything but <o:p></o:p></p><p class=MsoPlainText>> > will endeavour to provide help and squash bugs where I can. Also, <o:p></o:p></p><p class=MsoPlainText>> > please let me know if you use Bio-Linux for teaching or manage a <o:p></o:p></p><p class=MsoPlainText>> > large installation on your departmental server or computing lab.<o:p></o:p></p><p class=MsoPlainText>> > The more we can prove that people find this stuff useful, the more likely we are to get future funding!<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > I hope you enjoy using Bio-Linux 8.<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > TIM<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > --<o:p></o:p></p><p class=MsoPlainText>> > Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><o:p></o:p></p><p class=MsoPlainText>> > NERC Environmental Bioinformatics Centre<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > Centre for Ecology and Hydrology<o:p></o:p></p><p class=MsoPlainText>> > Maclean Bldg, Benson Lane<o:p></o:p></p><p class=MsoPlainText>> > Crowmarsh Gifford<o:p></o:p></p><p class=MsoPlainText>> > Wallingford, England<o:p></o:p></p><p class=MsoPlainText>> > OX10 8BB<o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> > <a href="http://nebc.nerc.ac.uk">http://nebc.nerc.ac.uk</a><o:p></o:p></p><p class=MsoPlainText>> > +44 1491 69 2705<o:p></o:p></p><p class=MsoPlainText>> > _______________________________________________<o:p></o:p></p><p class=MsoPlainText>> > Bio-Linux-announce mailing list<o:p></o:p></p><p class=MsoPlainText>> > <a href="mailto:Bio-Linux-announce@nebclists.nerc.ac.uk">Bio-Linux-announce@nebclists.nerc.ac.uk</a><o:p></o:p></p><p class=MsoPlainText>> > <a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-announce">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-announce</a><o:p></o:p></p><p class=MsoPlainText>> > <o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> --<o:p></o:p></p><p class=MsoPlainText>> Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><o:p></o:p></p><p class=MsoPlainText>> NERC Environmental Bioinformatics Centre<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> Centre for Ecology and Hydrology<o:p></o:p></p><p class=MsoPlainText>> Maclean Bldg, Benson Lane<o:p></o:p></p><p class=MsoPlainText>> Crowmarsh Gifford<o:p></o:p></p><p class=MsoPlainText>> Wallingford, England<o:p></o:p></p><p class=MsoPlainText>> OX10 8BB<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText>> <a href="http://nebc.nerc.ac.uk">http://nebc.nerc.ac.uk</a><o:p></o:p></p><p class=MsoPlainText>> +44 1491 69 2705<o:p></o:p></p><p class=MsoPlainText>> <o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>--<o:p></o:p></p><p class=MsoPlainText>Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><o:p></o:p></p><p class=MsoPlainText>NERC Environmental Bioinformatics Centre <o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText>Centre for Ecology and Hydrology<o:p></o:p></p><p class=MsoPlainText>Maclean Bldg, Benson Lane<o:p></o:p></p><p class=MsoPlainText>Crowmarsh Gifford<o:p></o:p></p><p class=MsoPlainText>Wallingford, England<o:p></o:p></p><p class=MsoPlainText>OX10 8BB <o:p></o:p></p><p class=MsoPlainText><o:p> </o:p></p><p class=MsoPlainText><a href="http://nebc.nerc.ac.uk">http://nebc.nerc.ac.uk</a><o:p></o:p></p><p class=MsoPlainText>+44 1491 69 2705<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Stephen P. Molnar, Ph.D. Life is a fuzzy set<o:p></o:p></p><p class=MsoNormal> (614)312-7528 (c) Stochastic and multivariate<o:p></o:p></p><p class=MsoNormal> Skype: smolnar1<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>