Re: FW: Bio linux download

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Re: FW: Bio linux download

Tony Travis
On 24/04/2019 14:55, Timms-Wilson, Tracey wrote:
> *From:*Shaun Allingham [mailto:[hidden email]]
> *Sent:* 24 April 2019 14:37
> *To:* Timms-Wilson, Tracey <[hidden email]>
> *Subject:* Bio linux download
>
> Hi, I am trying to download Biolinux on a USB stick but once i have
> finished the initial download the only option i get is to burn it onto a
> CD. Is there something i am missing?

Hi, Shaun.

Tracey forwarded your message to me and I've CC'ed my reply to the
Bio-Linux mailing list in case anyone else has the same problem.

We've done a 'point' release of Bio-Linux 8.0.8 that you can download:

> http://environmentalomics.org/bio-linux-8-0-8-2/

Please read the NERC/EOS documentation about how to create a USB-stick:

> http://environmentalomics.org/bio-linux-installation/

Please note that Bio-Linux 8.0.7/8 are both based on Ubuntu 14.04 LTS,
which will reach it's end of life this month (April 2019) so I do not
recommend using Bio-Linux 8, which is no longer supported by NERC/EOS.

I recommend downloading Ubuntu-MATE 18.04 LTS and creating a bootable
USB-stick from that, and use the USB-stick to install Ubuntu-MATE 18.04
permanently onto a hard disk (or an external USB disk):

> https://ubuntu-mate.org/download/

Then, boot from the hard disk and install "med-bio" and "med-bio-dev"
from the Debian-Med project onto the Ubuntu-MATE 18.04 instance:

   sudo -i
   apt update
   apt install med-bio med-bio-dev

[Note: There is a problem installing "metaphlan2" under Ubuntu 18.04]

Most of the packages in Bio-Linux 8 are now available in the Ubuntu
repository thanks to the work of the Debian-Med team. Please post a
message to the Debian-Med mailing list if you decide to try med-bio out.

I can provide you with a pre-release Bio-Linux 9-alpha 'live' USB-stick
based on Ubuntu-MATE 18.04 + packages from "med-bio" if you send me a
stamped addressed padded envelope to the address in my signature below.

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:[hidden email]

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Re: FW: Bio linux download

Graham Inggs-3
Hi Tony

On Wed, 24 Apr 2019 at 16:32, Tony Travis
<[hidden email]> wrote:
> [Note: There is a problem installing "metaphlan2" under Ubuntu 18.04]

Is this LP: #1777165 [1]?  Let's get this fixed, I'm happy to sponsor
a SRU [2] upload.

Regards
Graham

[1] https://pad.lv/1777165
[2] https://wiki.ubuntu.com/StableReleaseUpdates

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Re: FW: Bio linux download

Dylan Aïssi-3
Hi Graham,

Le mer. 24 avr. 2019 à 21:19, Graham Inggs <[hidden email]> a écrit :
>
> Is this LP: #1777165 [1]?  Let's get this fixed, I'm happy to sponsor
> a SRU [2] upload.
>

I am preparing the fix [1], I will ping you when it is ready.

Best,
Dylan

[1] https://salsa.debian.org/med-team/metaphlan2/commits/ubuntu/bionic

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Re: FW: Bio linux download

Graham Inggs-3
Hi

On Wed, 24 Apr 2019 at 21:30, Dylan Aïssi <[hidden email]> wrote:
> I am preparing the fix [1], I will ping you when it is ready.

Uploaded, thanks!

For future reference, the general procedure to get a fix into Ubuntu
is to attach a patch and subscribe 'ubuntu-sponsors' to the bug.

Regards
Graham

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Re: FW: Bio linux download

Tony Travis
On 24/04/2019 21:20, Graham Inggs wrote:
> Hi
>
> On Wed, 24 Apr 2019 at 21:30, Dylan Aïssi <[hidden email]> wrote:
>> I am preparing the fix [1], I will ping you when it is ready.
>
> Uploaded, thanks!
>
> For future reference, the general procedure to get a fix into Ubuntu
> is to attach a patch and subscribe 'ubuntu-sponsors' to the bug.

Hi, Graham and Dylan.

I reported the bug and provided a patch - What else should I have done?

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:[hidden email]

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Re: FW: Bio linux download

Graham Inggs-3
On Wed, 24 Apr 2019 at 23:42, Tony Travis
<[hidden email]> wrote:
> I reported the bug and provided a patch - What else should I have done?

Subscribing the 'ubuntu-sponsors' team to the bug would have made it
visible to someone who could have done the upload for you.

It's mostly only the packages supported by Canonical that have subscribers.

There's also a bot that finds patches, but it seems it only finds
attachments, not inline patches.

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Re: FW: Bio linux download

Tony Travis
On 25/04/2019 19:11, Graham Inggs wrote:

> On Wed, 24 Apr 2019 at 23:42, Tony Travis
> <[hidden email]> wrote:
>> I reported the bug and provided a patch - What else should I have done?
>
> Subscribing the 'ubuntu-sponsors' team to the bug would have made it
> visible to someone who could have done the upload for you.
>
> It's mostly only the packages supported by Canonical that have subscribers.
>
> There's also a bot that finds patches, but it seems it only finds
> attachments, not inline patches.

Hi, Graham.

OK, will do that next time :-)

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:[hidden email]

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Re: FW: Bio linux download

Tony Travis
In reply to this post by Dylan Aïssi-3
On 24/04/2019 20:29, Dylan Aïssi wrote:

> Hi Graham,
>
> Le mer. 24 avr. 2019 à 21:19, Graham Inggs <[hidden email]> a écrit :
>>
>> Is this LP: #1777165 [1]?  Let's get this fixed, I'm happy to sponsor
>> a SRU [2] upload.
>>
>
> I am preparing the fix [1], I will ping you when it is ready.
>
> Best,
> Dylan
>
> [1] https://salsa.debian.org/med-team/metaphlan2/commits/ubuntu/bionic

Hi, Dylan.

I've installed the "metaphlan2" package from Ubuntu "bionic-proposed"
successfully, with no errors reported. If "metaphlan2" is installed,
"med-bio" will install without errors in Ubuntu-MATE 18.04.2 LTS:

> ajt@beluga:~$ apt policy metaphlan2
> metaphlan2:
>   Installed: 2.7.5-1ubuntu1
>   Candidate: 2.7.5-1ubuntu1
>   Version table:
>  *** 2.7.5-1ubuntu1 400
>         400 http://gb.archive.ubuntu.com/ubuntu bionic-proposed/universe amd64 Packages
>         400 http://gb.archive.ubuntu.com/ubuntu bionic-proposed/universe i386 Packages
>         100 /var/lib/dpkg/status
>      2.7.5-1 500
>         500 http://gb.archive.ubuntu.com/ubuntu bionic/universe amd64 Packages
>         500 http://gb.archive.ubuntu.com/ubuntu bionic/universe i386 Packages

Please let me know if/when the broken version of "metaphlan2" will be
updated in the Ubuntu repositories?

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:[hidden email]

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Re: FW: Bio linux download

Dylan Aïssi-3
Hi Tony,

Le lun. 20 mai 2019 à 22:21, Tony Travis
<[hidden email]> a écrit :
> Hi, Dylan.
>
> I've installed the "metaphlan2" package from Ubuntu "bionic-proposed"
> successfully, with no errors reported. If "metaphlan2" is installed,
> "med-bio" will install without errors in Ubuntu-MATE 18.04.2 LTS:
>

Thanks for you report.

> Please let me know if/when the broken version of "metaphlan2" will be
> updated in the Ubuntu repositories?

You will be automatically notified when metaphlan2 will be updated in
Ubuntu repositories.
LP: #1777165 will switch to "Fix released".

Best,
Dylan