From tony.travis at minke-informatics.co.uk Mon May 1 18:19:31 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 1 May 2017 23:19:31 +0100 Subject: [Bio-linux-list] Bio-Linux MATE desktop Message-ID: <521a3e18-3629-37bc-a9f3-aa5821b658ee@minke-informatics.co.uk> Hi, I realise that some of us, myself included, like using the Ubuntu Unity desktop in Bio-Linux. In my case, this is mainly because it allows me to see a clear distinction between my local Unity desktop and a remote MATE desktop. Although I do like the MATE desktop, it's confusing when my local and remote desktops are the same. This is not an issue for people who use Windows or Mac versions of the "x2go" client because these desktops are very different to the remote MATE desktop. I've been evaluating Ubuntu-MATE 17.04 as the basis of a Bio-Linux 9-alpha version, with a view to using Ubuntu-MATE 18.04 LTS as the base distro for Bio-Linux 9. As part of my evaluation, I've created a MATE panel layout called "harmony" that resembles the layout I use in Unity: > https://www.dropbox.com/sh/y7spumkm4clctw6/AADu81HA5rjA8o8qQednHDAga?dl=0 If you're trying out Ubuntu-MATE 17.04, copy the .panel and .layout files into: /usr/share/mate-panel/layouts and use the MATE-tweak tool to select "harmony-tweak" to configure the "harmony" layout. Let me know what you think? Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tony.travis at minke-informatics.co.uk Wed May 3 07:42:16 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Wed, 3 May 2017 12:42:16 +0100 Subject: [Bio-linux-list] FW: New contact form received In-Reply-To: References: <2d09000dc94be5cd246f6a261c3d27d9@environmentalomics.org> Message-ID: <8d2a1892-6070-a5de-5cb8-afa90bdebd76@minke-informatics.co.uk> On 03/05/17 12:05, Timms-Wilson, Tracey wrote: > [...] >> You have received a new contact form message. >> Name : Rob Gilmore >> Email : rgilmore at umc.edu >> Message : Hi, >> I would like to request that the ETE Toolkit (ete3) be added to the software >> list. >> http://etetoolkit.org/download/ Hi, Rob. Tracey forwarded your message to me and I've sent my reply to the list. I've been trying out "Bioconda" on Bio-Linux 8 and it works very well: > https://bioconda.github.io/ You can install the ETE Toolkit on Bio-Linux 8 like this using Bioconda: > wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh > > # install Miniconda to /usr/local/miniconda2 > bash Miniconda2-latest-Linux-x86_64.sh > > # configure Miniconda for Python 2.7 > export PATH="/usr/local/miniconda2/bin:$PATH" > conda config --add channels conda-forge > conda config --add channels defaults > conda config --add channels r > conda config --add channels bioconda > > # install ETE > conda install ete3 > ete3 -h > usage: ete3 [-h] > {mod,extract,annotate,compare,view,ncbiquery,generate,evol,maptrees,build,version,upgrade-external-tools} > ... > > optional arguments: > -h, --help show this help message and exit > > AVAILABLE PROGRAMS: > {mod,extract,annotate,compare,view,ncbiquery,generate,evol,maptrees,build,version,upgrade-external-tools} [You need to use "sudo" if you want to install it all system-wide] HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tony.travis at minke-informatics.co.uk Thu May 4 09:28:21 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Thu, 4 May 2017 14:28:21 +0100 Subject: [Bio-linux-list] FW: Biolinux 7 In-Reply-To: References: <2338351493890083@web6g.yandex.ru> Message-ID: On 04/05/17 12:03, Timms-Wilson, Tracey wrote: > > > > -----Original Message----- > > From: Leonid Rusin [mailto:roussine at yandex.ru] > > Sent: 04 May 2017 10:28 > > To: Timms-Wilson, Tracey > > Subject: Biolinux 7 > > > > Hello, > > will be grateful if you let me know where is it possible to get the > BioLinux 7 > > distribution. Biolinux 8 is available from the main repository, > however version > > 7 is not. > > http://nebc.nerc.ac.uk/nebc_website_frozen/nebc.nerc.ac.uk//tools/bio- > > linux-7/bl_download.html > > > > Thank you in advance. > > Kind regards, > > Leonid > ________________________________ > 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. > ________________________________ > Hi, Leonid. Tracey forwarded your message to me and I've CC'ed my reply to the list. You can download Bio-Linux 7 from: > http://nebc.nerc.ac.uk/downloads/bio-linux-7-latest.iso > http://nebc.nerc.ac.uk/downloads/bio-linux-7-20131211.ova Note: Bio-Linux 7 is based on Ubuntu 12.04 LTS, which is no longer supported: > https://www.ubuntu.com/info/release-end-of-life I don't recommend using Bio-Linux 7 unless you have very good reason to. HTH, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From tony.travis at minke-informatics.co.uk Sun May 21 08:40:00 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Sun, 21 May 2017 13:40:00 +0100 Subject: [Bio-linux-list] Bio-Linux MATE desktop In-Reply-To: <521a3e18-3629-37bc-a9f3-aa5821b658ee@minke-informatics.co.uk> References: <521a3e18-3629-37bc-a9f3-aa5821b658ee@minke-informatics.co.uk> Message-ID: On 01/05/17 23:19, Tony Travis wrote: > [...] > I've been evaluating Ubuntu-MATE 17.04 as the basis of a Bio-Linux > 9-alpha version, with a view to using Ubuntu-MATE 18.04 LTS as the base > distro for Bio-Linux 9. [...] Hi, I've been using Ubuntu-MATE 17.04 as my day-to-day Linux on my laptop for three weeks now and, although I like it, I don't think it is stable enough to base an alpha release of Bio-Linux on it so I'm going back to using Ubuntu-MATE 16.04.2 LTS instead. Please post messages here if you use Ubuntu-MATE and let me know what you think about us using it for the next release of Bio-Linux 9. Thanks, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From raonyguimaraes at gmail.com Mon May 22 10:30:40 2017 From: raonyguimaraes at gmail.com (=?UTF-8?Q?Raony_Guimaraes_Corr=C3=AAa_Do_Carmo_Lisboa_Cardenas?=) Date: Mon, 22 May 2017 15:30:40 +0100 Subject: [Bio-linux-list] Bio-Linux MATE desktop In-Reply-To: References: <521a3e18-3629-37bc-a9f3-aa5821b658ee@minke-informatics.co.uk> Message-ID: Hi Tony, I had the same experience, ubuntu mate17.10 is not really ready for prime time yet ... I even had some issues with running virtualbox on it so I went straight back to 16.04 as my daily safe driver. Not really planing to upgrade for a while, I can say xenial is pretty stable at the moment and a good choice if you don't want any surprises. Can I ask what type of problems did you have ? Antergos is finally getting more attention so I would really recommend you try this if you want to get a more fresh and up to date linux experience. I tried your harmony panel which as I understand is just a fork from mutiny. I have to confess I don't really like the look, but I understand you want to make things as similar as possible to the previous version. That makes sense. Kind Regards. _____________________________________________ Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas PhD in Bioinformatics email: raonyguimaraes at gmail.com skype/hangouts: raonyguimaraes phone: +353 83 8389 337 _____________________________________________ On Sun, May 21, 2017 at 1:40 PM, Tony Travis < tony.travis at minke-informatics.co.uk> wrote: > On 01/05/17 23:19, Tony Travis wrote: > > [...] > > I've been evaluating Ubuntu-MATE 17.04 as the basis of a Bio-Linux > > 9-alpha version, with a view to using Ubuntu-MATE 18.04 LTS as the base > > distro for Bio-Linux 9. [...] > Hi, > > I've been using Ubuntu-MATE 17.04 as my day-to-day Linux on my laptop > for three weeks now and, although I like it, I don't think it is stable > enough to base an alpha release of Bio-Linux on it so I'm going back to > using Ubuntu-MATE 16.04.2 LTS instead. > > Please post messages here if you use Ubuntu-MATE and let me know what > you think about us using it for the next release of Bio-Linux 9. > > Thanks, > > Tony. > > -- > Minke Informatics Limited, Registered in Scotland - Company No. SC419028 > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) > tel. +44(0)19755 63548 http://minke-informatics.co.uk > mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list > -------------- next part -------------- An HTML attachment was scrubbed... URL: