[Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated

[Tony Travis]

On 15/02/17 01:25, Raony Guimaraes Corrêa Do Carmo Lisboa Cardenas wrote:
> Hi Tony,
> 
> Just would like to say a few words here. I sadly saw the development of
> Biolinux packages stalling on Launchpad <https://launchpad.net/bio-linux>.

Hi, Raony.

That link is to a bug-tracking page that Tim created during the
development of Bio-Linux 7, but few people actually used it because most
reported bugs on the mailing lists.

Please take a look at the PPA:

> https://launchpad.net/~nebc/+archive/ubuntu/bio-linux?field.series_filter=trusty

It is true that no packages have been updated in over a year, but Tim
was leading the development work and he has now left. Until recently, I
was too busy to take over and that is why development has stalled.

> I still believe there is a place for a Bioinformatics targeted linux distro.

Actually, there are already quite a few - Notable amongst which is
Debain-Med:

> https://alioth.debian.org/projects/debian-med

As you see there are quite a few project members and the Debian-Med team
have contributed significantly to the success of Bio-Linux.

> After speaking with Tim, I kind of felt he would like to see some of the
> effort that was put on Biolinux going to DebianMed. What's your position
> in terms of that ?

I agree with Tim, but that does not mean abandoning Bio-Linux!

What is important about Bio-Linux, in my view, is that it gives the
biologist a complete and fully-configured bioinformatics workstation
platform ready to run that requires little or no system administration
knowledge to use for bioinformatics work along with teaching materials
and supporting documentation.

Bio-Linux is, also, a platform on which you can run software packaged by
the Debian-Med team before it becomes available in the Ubuntu
repositories automatically from the Debian 'unstable' release:

> https://launchpad.net/ubuntu/+source/debian-med

Debian-Med have been extremely helpful and supportive towards Bio-Linux
and we have jointly organised Debian-Med 'Sprints'. See 'Meetings' at:

> https://wiki.debian.org/DebianMed

[I organised the 4th one in Scotland in 2014]

> Do you have any estimate for the amount of money you would need to raise
> to keep the development of Biolinux ?

I discussed this with Tim and we think it would take a full-time
post-doc about six months to create Bio-Linux 9 and update all the
teaching materials and documentation.

>  Have you considered using Patreon ?

No, not heard of that?

> Please don't let this project die! What's the plan and timeline to start
> upgrading the packages to Xenial ? 

I'm doing it already, privately, on a small scale. I'm waiting to see
the outcome of funding requests before taking the project any further.

Please note that Steve Moss has forked Tim's "build-bio-linux" GitHub
repository as a starting point for community development of Bio-Linux:

> https://github.com/Bio-Linux

@Steve - Please let the list know what your plans are on GitHub?

> My biggest suggestion would be to try to base the next release of
> Biolinux on Ubuntu Mate <https://ubuntu-mate.org> 16.04, the lead
> developer also lives in the UK (Martin Wimpress
> <https://plus.google.com/+MartinWimpress>).

You don't need to do that because the present version can be used with
either a Unity or MATE local desktop. However, the only remote desktop
supported is MATE because Unity requires hardware acceleration that is
not available on a remote "x2go" session and MATE does not require it.

> Maybe we should even
> consider targeting the next 18.04 LTS release ... This branch will
> effectively be created in October of this year.

I don't see the point - The current 14.04 LTS will be supported until
April 2019 and no End-of-Life date has been announced for 16.04 LTS.

> https://wiki.ubuntu.com/Releases

I'm only considering development of Bio-Linux 9 on Ubuntu 16.04 LTS.

> What about snaps ? Have you considered packaging the current and future
> bioinformatic tools we have using that ?

One of the reasons that NERC/EOS supported the development of Bio-Linux
was to promote "Reproducible Research". From that point of view, I think
that lightweight containers like "Docker" and "SNAP" are a good idea.
However, The isolation of dependencies comes at a cost: Like the
difference between static and dynamic linking of executable binaries. it
is always a compromise between requiring libraries to be present, but
being able to share them between executables, and having statically
linked executables with no external dependencies but unable to share.

To me, this is a microcosm of hiding application dependencies in
'lightweight' containers... I'm not against it, but I am sceptical that
it will help in our use-case :-)

> What's the road map for the project ? What are the most important
> packages you guys are planning to start upgrading?

For me, it's QIIME, which has been a problem for some of my friends and
colleagues who want to use it under Bio-Linux 8 upgraded to Ubuntu 16.04
LTS. The other major disaster area is Galaxy, but I've not looked at it
yet. Otherwise, I want to weed out any use of /usr/local by any
Bio-Linux packages (which is bad practice, but was a pragmatic way of
building the original binary packages before advice from Debian-Med).
Best practice is to reserve /usr/local for manually installed software.

> I'm currently living in Ireland, so I would love to visit you guys
> anytime to have a more profound conversation about this things.

OK, my address is in my signature below and I live next to a pub!

Bye,

  Tony.

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