From tony.travis at minke-informatics.co.uk Sun Oct 14 20:28:29 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 15 Oct 2018 01:28:29 +0100 Subject: [Bio-linux-list] Bio-Linux 9 Message-ID: Hi, I'm now back from Milan and working part-time at the University of Aberdeen again. We are upgrading all our Bio-Linux 8 (Ubuntu 14.04 LTS) machines to Ubuntu-MATE 18.04 LTS + med-bio + med-bio-dev as prototypes to use during the development of Bio-Linux 9. So far the only problem I've encountered is a bug in the "metaphlan2" package that I reported here and Andreas acted on. However, the updated package is not yet in the Debian Sid repository that Ubuntu is based on. Installing "med-bio" under Ubuntu-MATE 18.04 currently fails installing "metaphlan2", but that problem can be resolved by manually installing an updated version of the package from a .deb locally. I really appreciate the work that the Debian-Med team have been doing to incorporate many of the 'missing' packages from Bio-Linux 8 because it makes development of Bio-Linux 9 based on Ubuntu-MATE 18.04 LTS and the packages from "med-bio" a practical proposition. 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 tony.travis at minke-informatics.co.uk Sun Oct 14 20:41:15 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 15 Oct 2018 01:41:15 +0100 Subject: [Bio-linux-list] Bio-Linux 9 In-Reply-To: References: Message-ID: <721defb7-a5e3-d4b9-1ad4-ef30082ffc55@minke-informatics.co.uk> On 15/10/18 01:28, Tony Travis wrote: > [...] > So far the only problem I've encountered is a bug in the "metaphlan2" > package that I reported here and Andreas acted on. However, the updated > package is not yet in the Debian Sid repository that Ubuntu is based on. > > Installing "med-bio" under Ubuntu-MATE 18.04 currently fails installing > "metaphlan2", but that problem can be resolved by manually installing an > updated version of the package from a .deb locally. Hi, I CC'ed my previous message from the debian-med list to the bio-linux list because it might be of interest to any Bio-Linux 8 users who are thinking about upgrading to Ubuntu 18.04 LTS. My advice is NOT to try to upgrade Bio-Linux 8, but do a clean install of Ubuntu-MATE 18.04 LTS and then install the "med-bio" + "med-bio-dev" packages, because that is what Bio-Linux 9 will be based on. 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 dksamuel2 at gmail.com Tue Oct 16 05:56:57 2018 From: dksamuel2 at gmail.com (dksamuel2) Date: Tue, 16 Oct 2018 15:26:57 +0530 Subject: [Bio-linux-list] Bio-Linux 9 In-Reply-To: <721defb7-a5e3-d4b9-1ad4-ef30082ffc55@minke-informatics.co.uk> References: <721defb7-a5e3-d4b9-1ad4-ef30082ffc55@minke-informatics.co.uk> Message-ID: Sir will you also please make a version for WSL to run on MS windows 10 as that platform is also very much interesting, thanks Dr.D.K.Samuel , Bangalore, India On Mon, Oct 15, 2018 at 6:11 AM Tony Travis < tony.travis at minke-informatics.co.uk> wrote: > On 15/10/18 01:28, Tony Travis wrote: > > [...] > > So far the only problem I've encountered is a bug in the "metaphlan2" > > package that I reported here and Andreas acted on. However, the updated > > package is not yet in the Debian Sid repository that Ubuntu is based on. > > > > Installing "med-bio" under Ubuntu-MATE 18.04 currently fails installing > > "metaphlan2", but that problem can be resolved by manually installing an > > updated version of the package from a .deb locally. > > Hi, > > I CC'ed my previous message from the debian-med list to the bio-linux > list because it might be of interest to any Bio-Linux 8 users who are > thinking about upgrading to Ubuntu 18.04 LTS. > > My advice is NOT to try to upgrade Bio-Linux 8, but do a clean install > of Ubuntu-MATE 18.04 LTS and then install the "med-bio" + "med-bio-dev" > packages, because that is what Bio-Linux 9 will be based on. > > 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 > _______________________________________________ > 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: From tony.travis at minke-informatics.co.uk Tue Oct 16 08:02:34 2018 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 16 Oct 2018 13:02:34 +0100 Subject: [Bio-linux-list] Bio-Linux 9 In-Reply-To: References: <721defb7-a5e3-d4b9-1ad4-ef30082ffc55@minke-informatics.co.uk> Message-ID: <29ef27e3-741a-5e1c-d740-1a15af6becd8@minke-informatics.co.uk> On 16/10/18 10:56, dksamuel2 wrote: > Sir will you also please make a version for WSL to run on MS windows 10 > as that platform is also very much interesting, thanks Dr.D.K.Samuel , > Bangalore, India Hi, I've thought about using WSL, but it is really only for command-line programs and not yet a fully supported part of Windows 10. You have to specifically enable it. However, the Ubuntu bash interface works well under WSL for Windows 10 and, if you have no alternative, it's as close as you can get to using Ubuntu under Windows without a VM. Cygwin is a good alternative, but does not support the Ubuntu/Debian repositories. Maybe you would like to volunteer and try this under WSL for Windows 10: apt update apt install med-bio Please post your experiences here. 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 dksamuel2 at gmail.com Tue Oct 16 21:25:02 2018 From: dksamuel2 at gmail.com (dksamuel2) Date: Wed, 17 Oct 2018 06:55:02 +0530 Subject: [Bio-linux-list] Bio-Linux 9 In-Reply-To: <29ef27e3-741a-5e1c-d740-1a15af6becd8@minke-informatics.co.uk> References: <721defb7-a5e3-d4b9-1ad4-ef30082ffc55@minke-informatics.co.uk> <29ef27e3-741a-5e1c-d740-1a15af6becd8@minke-informatics.co.uk> Message-ID: Yes Sir I will try and report. Thanks Samuel On Tue 16 Oct, 2018, 5:32 PM Tony Travis, < tony.travis at minke-informatics.co.uk> wrote: > On 16/10/18 10:56, dksamuel2 wrote: > > Sir will you also please make a version for WSL to run on MS windows 10 > > as that platform is also very much interesting, thanks Dr.D.K.Samuel , > > Bangalore, India > > Hi, > > I've thought about using WSL, but it is really only for command-line > programs and not yet a fully supported part of Windows 10. You have to > specifically enable it. However, the Ubuntu bash interface works well > under WSL for Windows 10 and, if you have no alternative, it's as close > as you can get to using Ubuntu under Windows without a VM. Cygwin is a > good alternative, but does not support the Ubuntu/Debian repositories. > > Maybe you would like to volunteer and try this under WSL for Windows 10: > > apt update > apt install med-bio > > Please post your experiences here. > > 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: