From spaporovic at fh-bielefeld.de Wed May 21 12:27:06 2014 From: spaporovic at fh-bielefeld.de (spaporovic at fh-bielefeld.de) Date: Wed, 21 May 2014 18:27:06 +0200 Subject: [Bio-linux-dev] BioLinux derivative Message-ID: <537CD3DA.9010908@fh-bielefeld.de> Hello, its a task I think about since some years: I my mind BioLinux is a very good enviroment for bioinformatics. Beside this I have some contacts to medical care services. They need some different software for their work, so BioLinux is not exactly what they want. In 2012 I have already done a derivative of Ubuntu for Physics. I have made this as a little present for some physicist I know. They were happy:). But it was not designed for going in the wild, so it is not public available. This time I would like to do this a little bit broader and as already mentioned above for medical services. I am not so sure if I start with Ubuntu again or this time, because it has already got a bunch of extra work and refinement, with BioLinux. Tim, you have derived BioLinux7 in 2012 from precise. I would like to start with my work on a more up to date LTS. Well, it is Ubuntu14.04 I have an eye on. Have you already started to design BioLinux8, probably on the 14.04 basis? For my project, if I realy do it, I would like to establish a default unity-desktop with cairo-dock enabled. Also some additional compiz features may be used, but I am careful with this in mind. It should be kept at whole as a office desktop. Some medical specific packages like CMS(Clinical Managment System)should be integrated from a custom repository. I think about to integrate some of them directly in the unity-desktop with the web-content abilities of unity, as far as they work with a web-interface. It seems to be not very complicated to do this, like the ubuntu documentation shows, but keeps as an add-on, because of the additional time invest. Beside this, adoptions to the system, like removing the Ubuntu brandings or make some changes to the Software-Center, you have already done for BioLinux7, are necessary also. I remember that there where some documents available from you how to make the derivation for BioLinux from Ubuntu, even when they only focus on BioLinux6. Do you have this provided also for the more recent OS-Version(s)? Greetings Sasa Paporovic From tony.travis at abdn.ac.uk Thu May 22 05:18:56 2014 From: tony.travis at abdn.ac.uk (Tony Travis) Date: Thu, 22 May 2014 10:18:56 +0100 Subject: [Bio-linux-dev] BioLinux derivative In-Reply-To: <537CD3DA.9010908@fh-bielefeld.de> References: <537CD3DA.9010908@fh-bielefeld.de> Message-ID: <537DC100.4030209@abdn.ac.uk> On 21/05/14 17:27, spaporovic at fh-bielefeld.de wrote: > [...] > Tim, you have derived BioLinux7 in 2012 from precise. I would like to > start with my work on a more up to date LTS. Well, it is Ubuntu14.04 I > have an eye on. Have you already started to design BioLinux8, probably > on the 14.04 basis? > [...] > I remember that there where some documents available from you how to > make the derivation for BioLinux from Ubuntu, even when they only focus > on BioLinux6. Do you have this provided also for the more recent > OS-Version(s)? Hi, Sasa. I've upgraded one of my Bio-Linux 7 machines to Ubuntu 14.04 with few problems. You have to change some of the third-party repositories Tim has used from "precise" to "trusty" - In particular the CRAN repo. I'm compiling a how-to just now ;-) Bye, Tony. -- Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis The University of Aberdeen is a charity registered in Scotland, No SC013683. Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683. From tbooth at ceh.ac.uk Thu May 22 05:23:38 2014 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 22 May 2014 10:23:38 +0100 Subject: [Bio-linux-dev] BioLinux derivative In-Reply-To: <537CD3DA.9010908@fh-bielefeld.de> References: <537CD3DA.9010908@fh-bielefeld.de> Message-ID: <1400750618.2467.13.camel@balisaur> Hi Sasa, Yes, I'm working on Bio-Linux 8 which is indeed based on 14.04. Most of the custom modifications are captured within the deb packages, but I do still have to add some modifications directly to the ISO image when I re-pack it. The notes on what I did for BL7 are here: http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/devinfo I'll post a modified version for BL8 once I have it working, but there is not that much difference between the versions, from a developers point of view, so the stuff linked above mostly still applies. If I were you I'd start with regular Ubuntu as your base. Virtually everything you would want from Bio-Linux is in a .deb so you can just install the packages as you want them, and things like the rebranding of the boot menu and the desktop are things you'll want to do for yourself anyway. I suggest you download, unpack and take a look at bio-linux-themes-v7, bio-linux-plymouth-theme, and bio-linux-unity-lens from the repo here: http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/all/ I also have a new new package called bio-linux-cruft-killer that aims to strip out some of the clutter from the newer Unity desktop. This needs a little more testing but it seems to work. Hope that is useful info. TIM On Wed, 2014-05-21 at 17:27 +0100, spaporovic at fh-bielefeld.de wrote: > Hello, > > its a task I think about since some years: > > I my mind BioLinux is a very good enviroment for bioinformatics. Beside > this I have some contacts to medical care services. They need some > different software for their work, so BioLinux is not exactly what they > want. > > In 2012 I have already done a derivative of Ubuntu for Physics. I have > made this as a little present for some physicist I know. They were > happy:). But it was not designed for going in the wild, so it is not > public available. > > This time I would like to do this a little bit broader and as already > mentioned above for medical services. > > I am not so sure if I start with Ubuntu again or this time, because it > has already got a bunch of extra work and refinement, with BioLinux. > > Tim, you have derived BioLinux7 in 2012 from precise. I would like to > start with my work on a more up to date LTS. Well, it is Ubuntu14.04 I > have an eye on. Have you already started to design BioLinux8, probably > on the 14.04 basis? > > For my project, if I realy do it, I would like to establish a default > unity-desktop with cairo-dock enabled. Also some additional compiz > features may be used, but I am careful with this in mind. It should be > kept at whole as a office desktop. Some medical specific packages like > CMS(Clinical Managment System)should be integrated from a custom > repository. I think about to integrate some of them directly in the > unity-desktop with the web-content abilities of unity, as far as they > work with a web-interface. It seems to be not very complicated to do > this, like the ubuntu documentation shows, but keeps as an add-on, > because of the additional time invest. > > Beside this, adoptions to the system, like removing the Ubuntu brandings > or make some changes to the Software-Center, you have already done for > BioLinux7, are necessary also. > > I remember that there where some documents available from you how to > make the derivation for BioLinux from Ubuntu, even when they only focus > on BioLinux6. Do you have this provided also for the more recent > OS-Version(s)? > > Greetings > > Sasa Paporovic > > _______________________________________________ > Bio-Linux-dev mailing list > Bio-Linux-dev at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From spaporovic at fh-bielefeld.de Sat May 24 08:37:11 2014 From: spaporovic at fh-bielefeld.de (spaporovic at fh-bielefeld.de) Date: Sat, 24 May 2014 14:37:11 +0200 Subject: [Bio-linux-dev] BioLinux derivative In-Reply-To: <1400750618.2467.13.camel@balisaur> References: <537CD3DA.9010908@fh-bielefeld.de> <1400750618.2467.13.camel@balisaur> Message-ID: <53809277.8010602@fh-bielefeld.de> Hello Tony, hello Tim, thank you both for your statements and help. I have just take a look on the stuff, so it seems possible to do that for me. Well, it will take a while until I will have a first working .iso. I would appreciate it if it would be possible for you to take a look at it, when it is done. But this will be only one point on my TODO-List, beside a start-up founding around VirtueMart(I am an author of a commercial instruction video - only in german), recording of two new instruction videos, one nearly finished, ... and... well, when one of you have found a solution for getting more hours out of a 24 hour day, you may give me a hint, if you like:). For know I starting in my holiday. Wish you a nice spring/summer, Sasa Paporovic P.S: Hi Tony. I would like to read your How-to. May be you want to send me a link, when its done. Greetins, Sasa Am 22.05.2014 11:23, schrieb Tim Booth: > Hi Sasa, > > Yes, I'm working on Bio-Linux 8 which is indeed based on 14.04. Most of > the custom modifications are captured within the deb packages, but I do > still have to add some modifications directly to the ISO image when I > re-pack it. The notes on what I did for BL7 are here: > > http://nebc.nerc.ac.uk/tools/bio-linux/other-bl-docs/devinfo > > I'll post a modified version for BL8 once I have it working, but there > is not that much difference between the versions, from a developers > point of view, so the stuff linked above mostly still applies. > > If I were you I'd start with regular Ubuntu as your base. Virtually > everything you would want from Bio-Linux is in a .deb so you can just > install the packages as you want them, and things like the rebranding of > the boot menu and the desktop are things you'll want to do for yourself > anyway. > > I suggest you download, unpack and take a look at bio-linux-themes-v7, > bio-linux-plymouth-theme, and bio-linux-unity-lens from the repo here: > http://nebc.nerc.ac.uk/bio-linux/dists/unstable/bio-linux/all/ > > I also have a new new package called bio-linux-cruft-killer that aims to > strip out some of the clutter from the newer Unity desktop. This needs > a little more testing but it seems to work. > > Hope that is useful info. > > TIM > > On Wed, 2014-05-21 at 17:27 +0100, spaporovic at fh-bielefeld.de wrote: >> Hello, >> >> its a task I think about since some years: >> >> I my mind BioLinux is a very good enviroment for bioinformatics. Beside >> this I have some contacts to medical care services. They need some >> different software for their work, so BioLinux is not exactly what they >> want. >> >> In 2012 I have already done a derivative of Ubuntu for Physics. I have >> made this as a little present for some physicist I know. They were >> happy:). But it was not designed for going in the wild, so it is not >> public available. >> >> This time I would like to do this a little bit broader and as already >> mentioned above for medical services. >> >> I am not so sure if I start with Ubuntu again or this time, because it >> has already got a bunch of extra work and refinement, with BioLinux. >> >> Tim, you have derived BioLinux7 in 2012 from precise. I would like to >> start with my work on a more up to date LTS. Well, it is Ubuntu14.04 I >> have an eye on. Have you already started to design BioLinux8, probably >> on the 14.04 basis? >> >> For my project, if I realy do it, I would like to establish a default >> unity-desktop with cairo-dock enabled. Also some additional compiz >> features may be used, but I am careful with this in mind. It should be >> kept at whole as a office desktop. Some medical specific packages like >> CMS(Clinical Managment System)should be integrated from a custom >> repository. I think about to integrate some of them directly in the >> unity-desktop with the web-content abilities of unity, as far as they >> work with a web-interface. It seems to be not very complicated to do >> this, like the ubuntu documentation shows, but keeps as an add-on, >> because of the additional time invest. >> >> Beside this, adoptions to the system, like removing the Ubuntu brandings >> or make some changes to the Software-Center, you have already done for >> BioLinux7, are necessary also. >> >> I remember that there where some documents available from you how to >> make the derivation for BioLinux from Ubuntu, even when they only focus >> on BioLinux6. Do you have this provided also for the more recent >> OS-Version(s)? >> >> Greetings >> >> Sasa Paporovic >> >> _______________________________________________ >> Bio-Linux-dev mailing list >> Bio-Linux-dev at nebclists.nerc.ac.uk >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev