[ensembl-dev] Perl Version Upgrade

Tue Jan 14 09:59:18 GMT 2014

Hi Andy,

We use Ensembl in much the same way as Ed describes, i.e. a tool in a
larger heterogenous pool. Although perl 5.8 is the 'officially' supported
Perl for Ensembl, we have successfully used the system perl on Ubuntu 10.04
and latterly 12.04 (i.e. Perl 5.14) . At some point Ensembl were bound to
update the 'official' Perl for all sorts of good reasons (performance,
security, features), and 5.14 seems like a good, stable, recent(ish)
version to decide on.

Best,

Will

On Mon, Jan 13, 2014 at 11:46 PM, gray_ed <gray_ed at hotmail.com> wrote:

>  So 5.10 is the natural ceiling?
>
>
> -------- Original message --------
> From: Keiran Raine
> Date:01/13/2014 4:55 PM (GMT-05:00)
> To: dev at ensembl.org
> Subject: Re: [ensembl-dev] Perl Version Upgrade
>
>  Sorry correction, it's 5.10+!
>
> Sent from my Android phone using TouchDown (www.nitrodesk.com)
>
>
> -----Original Message-----
> From: Andy Yates [ayates at ebi.ac.uk]
> Received: Monday, 13 Jan 2014, 20:56
> To: Ensembl developers list [dev at ensembl.org]
> Subject: Re: [ensembl-dev] Perl Version Upgrade
>
> Hi Keiran
>
> Thanks for the info. It seems that 5.14 is a natural ceiling for the
> moment ...
>
> Andy
>
> Sent from my mobile.
>
> > On 13 Jan 2014, at 20:17, "Keiran Raine" <kr2 at sanger.ac.uk> wrote:
> >
> > Hi Andy,
> >
> > Just a quick note about the upper limit for GBrowse. Perl 5.16+ is an
> issue for systems wishing to have full control over remote tracks due to
> the loss of Safe::World support.
> >
> > Regards,
> > Keiran
> >
> > Please excuse any brevity or typographic errors, sent from my Android
> phone using TouchDown (www.nitrodesk.com)
> >
> > -----Original Message-----
> > From: Andy Yates [ayates at ebi.ac.uk]
> > Received: Monday, 13 Jan 2014, 17:02
> > To: Ensembl developers list [dev at ensembl.org]
> > Subject: Re: [ensembl-dev] Perl Version Upgrade
> >
> > Hi Ed,
> >
> > I don't think we need to worry about semantics of users vs. developers
> both are equally affected by this change. To cover our now revised plan:
> >
> > 1). Release 75: We will require Perl 5.10+
> > 2). Release 76: We will require Perl 5.14+
> >
> > This hopefully will give Ensembl the freedom to adopt newer versions of
> syntax we feel is positive for the project whilst at the same time not
> abandoning users in a single swoop. We really do want feedback on this plan
> though from anyone on this list. I am confident that the 1st migration is a
> positive step.
> >
> > So why that decision. Now you will have to forgive my ignorance here a
> little about the tools you've mentioned since my own personal experience
> with their management is very limited. However I do know this much about
> the examples you've given:
> >
> > - Gbrowse is shipped as a Debian package with dependencies. That
> specifically declares a Perl 5.10>= dependency [1]. Looking at Debian
> though their latest Perl version is 5.18 & Gbrowse does not seem to give an
> upper limit on support
> > - CloudBioLinux is an Ubuntu based distro with versions 12.04+ [2]. We
> know from our own investigations that 12.04+ ships with 5.14 out of the box
> > - CloudMan & Starcluster are both Python based projects. StarCluster
> mentions that it's current AMIs are built from Ubuntu 12.04 [3]
> > - BioLinux is also based off 12.04 Ubuntu images [4]
> > - I have been developing Ensembl using Perl 5.14 for over 2 years & in
> that time I have not seen a serious issue with BioPerl & later versions.
> Though Chris Fields does subscribe to this list so maybe he can shine some
> more info on this issue.
> > - We are also trying to use Travis-CI which brings multiple Perl version
> continuous integration meaning we should be able to pick up on issues long
> before they become serious.
> >
> > From those examples we've explored all support versions of Perl greater
> than 5.10 & it seems that all would support a 5.14 based environment. We
> have thought about end users and we want to make these changes because we
> believe that software should not stagnate and fixing software version
> dependencies is not positive for anyone. It is not in our interest to annoy
> any Ensembl user just for the sake of it and we are more than aware of
> everyone's ever increasing data volumes.
> >
> > Regards,
> >
> > Andy
> >
> > p.s.
> >
> > As you said Perlbrew is primarily used for multiple Perl management on a
> per-user basis but we have seen it used very successfully as a shared
> deployment area. Ensembl Genomes uses a shared Perlbrew installation as
> their production code. Perlbrew also gives a very useful away of installing
> newer versions of Perl. Since Perl now releases a major version every year
> being able to move along with versions is important not only for developers
> but for users as later versions can offer improved runtime & lower memory
> consumption. Creating a shared installation is as simple as running
> (assuming we will install this to /opt/perl5):
> >
> > export PERLBREW_ROOT=/opt/perl5
> > curl -kL http://install.perlbrew.pl | bash
> >
> > Perlbrew prints instructions about how to add this new location to your
> shell environment after which all the standard commands work including the
> very excellent cpanminus (cpanm).
> >
> > [1] - http://packages.debian.org/sid/gbrowse
> > [2] -
> http://thecloudmarket.com/search?search_term=cloudbiolinux&order=updated_at%20desc
> > [3] - http://star.mit.edu/cluster/
> > [4] - http://nebc.nerc.ac.uk/tools/bio-linux
> >
> > ------------
> > Andrew Yates - Ensembl Support Coordinator
> > European Bioinformatics Institute (EMBL-EBI)
> > European Molecular Biology Laboratory
> > Wellcome Trust Genome Campus
> > Hinxton
> > Cambridge CB10 1SD
> > Tel: +44-(0)1223-492538
> > Fax: +44-(0)1223-494468
> > http://www.ensembl.org/
> >
> > On 13 Jan 2014, at 15:29, Ed Gray <gray_ed at hotmail.com> wrote:
> >
> > > Dear Andy,
> > >
> > > We are primarily a user not a developer of bioinformatics. I
> understand that many of the rest of you are developers since this is a
> developer's list, although I believe that users should monitor this list to
> get help and understand potential problems like the perl issue we've been
> discussing. I wonder how many here are primarily users vs. developers??
> > >
> > > We are not familiar with perlbrew, but the homepage described it as
> "perlbrew is a tool to manage multiple perl installations in your $HOME
> directory." This is not usable for us in any reasonable sense since we
> integrate many tools to provide the functionality we need and we run the
> tools in pipelines that string these tools together.
> > >
> > > Ensembl is a primary tool, we love it and we love you! But ensembl not
> the only tool, and forcing us to go to a new release of perl that is not
> widely supported by all of the other tools is a significant burden that I
> believe will throw us and many of the 'user' class individuals, into an
> unknowable chaos. It might be great, but it might lead to problems,
> currently that seems unknown.
> > >
> > > Of course no path forward is easy, upgrades in the underlying OS and
> base tools are important for a number of reasons. It would seem to me that
> we could arrive at a list of software that will no longer be supportable in
> a pipeline under perl 5.18 (or whatever release you finally decide is
> needed by the users).
> > >
> > > For instance, many of us use GBrowse and GMOD in general. Almost all
> use use bioperl and that seems to be the common denominator for many
> bio-apps on perl. Lots use some cluster management software, be it
> CloudMan, Starcluster, or directly using SGE. I imagine that many use
> Galaxy and some CloudBiolinux. I could go on, but there certainly are other
> categories of software that many folks use (such as genome and
> transcrtiptome assemblers, comparators, annotators, etc).
> > >
> > > I am certain it is not in ensembl's best interests to cause problems
> for folks that use these tools, so which are supported on what versions of
> perl?
> > >
> > > Prior to setting your user base into disarray by requiring us to move
> to a perl release for experimental features, I think it wise to at minimum
> query your user base to see what difficulties this causes them. How many
> users are "OK" with perlbrew? Are you essentially marginalizing yourselves
> if you create an environment that is incompatible with other popular
> environments (e.g. GMOD/Gbrowse, Galaxy etc.)?
> > >
> > > I sense a major disturbance in the force, so to say using StarWars
> lingo, and this is not an area where I have seen you consider items outside
> of ensembl's internal needs.  Maybe you have and I don't see it, that is
> possible. But is there a chance that you should look at this from your
> user's perspective prior to taking a plunge that may have grave
> consequences.
> > >
> > > As a user, I don't have the resources to do this analysis in a few
> weeks, we are busy doing other things that will keep our management happy.
> Hitting ongoing projects with unexpected delays and resource needs gives
> the whole bioinformatics community a black eye.
> > >
> > > Best Regards,
> > > Ed Gray
> > > Executive Director, Xenobiology and Synthetic Genomics
> > > United Therapeutics Corp.
> > > www.unither.com
> > >
> > >
> > >
> > >
> > >
> > > > From: ayates at ebi.ac.uk
> > > > Date: Fri, 10 Jan 2014 15:10:20 +0000
> > > > To: dev at ensembl.org
> > > > Subject: Re: [ensembl-dev] Perl Version Upgrade
> > > >
> > > > Hi Chris, Jan & Jennifer
> > > >
> > > > Firstly thank you for all of your contributions. Just to let me
> summarise my current thinking on all the topics raised:
> > > >
> > > > 1). Thank you for the warning about 5.18 and the use of experimental
> features. What is more worrying is that features like smart matching are
> going through significant changes at the moment meaning should we use them
> we need to be aware of where & make sure we can react in our code
> accordingly [1]. This will probably require us making the experimental
> module a requirement [2].
> > > >
> > > > 2). As Jan & Chris have mentioned (and I did in my previous email)
> Perlbrew is a very good tool for binary management. We are working on a
> short guide similar to the one produced for OSX to guide users how to build
> Perlbrew and a Perl version on Ubuntu boxes. Hopefully this will prove
> useful.
> > > >
> > > > 3). Package management is a red herring here but I do want to say
> one thing about this. Producing a CPAN based version of Ensembl at the
> moment, IMHO, is a bad idea. Software releases are heavily tied to the data
> sets. Creating and releasing a CPAN distro (onto CPAN) only increases those
> chances of a sysadmin deciding to install Ensembl because a user asked them
> to do so. Tools like Carton & Pinto are amazing tools and making Tasks
> available for this would be a really nice way of allowing people to use
> them. We are investigating new methods of distribution
> > > >
> > > > I'm in the process of talking to people internally to take on board
> the comments raised here.
> > > >
> > > > Andy
> > > >
> > > > [1] - https://rt.perl.org/Public/Bug/Display.html?id=119317
> > > > [2] - https://metacpan.org/pod/experimental
> > > > ------------
> > > > Andrew Yates - Ensembl Support Coordinator
> > > > European Bioinformatics Institute (EMBL-EBI)
> > > > European Molecular Biology Laboratory
> > > > Wellcome Trust Genome Campus
> > > > Hinxton
> > > > Cambridge CB10 1SD
> > > > Tel: +44-(0)1223-492538
> > > > Fax: +44-(0)1223-494468
> > > > http://www.ensembl.org/
> > > >
> > > > On 9 Jan 2014, at 22:38, "Fields, Christopher J" <
> cjfields at illinois.edu> wrote:
> > > >
> > > > > Was supposed to be:
> > > > >
> > > > > ...
> > > > > 're: Task modules, for Bioperl, we intend on splitting core into
> components and bundling them into tasks for various purposes. The eventual
> intent is to make it so you only install the components you need, instead
> of everything’
> > > > >
> > > > > But everyone probably worked that one out.
> > > > >
> > > > > chris
> > > > >
> > > > > On Jan 9, 2014, at 4:28 PM, Fields, Christopher J <
> cjfields at illinois.edu> wrote:
> > > > >
> > > > >> I completely agree. FWIW, this is what we also do locally here in
> Illinois (UIUC). Can’t recommend perlbrew and cpanm enough; these in
> combination with env. modules are quite nice on the maintenance end as well
> (e.g. in cases where some applications need a thread-compiled vs.
> non-thread-compiled perl, for instance). I also recommend a look into Pinto
> and Carton.
> > > > >>
> > > > >> re: Task modules, for Bioperl, we intend on splitting core into
> components and bundling them into tasks for various purposes. The eventual
> intent is to make it so you only install the components you need, instead
> of
> > > > >>
> > > > >> I do want to point out something: IIRC, one of the intents from
> the Ensembl developers on requiring a newer version of perl is to take
> advantage of newer language functionality (smart match, switch statements,
> state variables, etc). I should point out that these are now marked as
> ‘experimental’ in the latest version of perl (v5.18), so they will trigger
> warnings unless you set up the proper pragma for using them.
> > > > >>
> > > > >> chris
> > > > >>
> > > > >> On Jan 9, 2014, at 3:51 PM, Jan Vogel <jan.vogel at gmail.com>
> wrote:
> > > > >>
> > > > >>>
> > > > >>> Hi Andy, Jennifer et al,
> > > > >>>
> > > > >>> performing a OS upgrade just to upgrade the perl version seems
> like overkill to me.
> > > > >>>
> > > > >>> We here in San Francisco use a set up which allows us to run
> ensembl related analyses on
> > > > >>> various perl version, i.e. 5.14.2, 5.16.3 and most recently
> 5.18.1
> > > > >>>
> > > > >>> The whole perl environments are controlled via so called
> "furlani" modules - a system which
> > > > >>> has been developed by John Furlani and Peter Osel - see
> http://modules.sourceforge.net/
> > > > >>>
> > > > >>> In a multi-user environment, the Furlani modules help a lot to
> organize and set up environments for various different tasks and users - I
> strongly recommend to check this out.
> > > > >>>
> > > > >>> The system can be easily extended to load other environments as
> well - it provides dynamic modification
> > > > >>> of the user's environment - not only for perl, but also for
> users who like to set up their R environment or other.
> > > > >>> Of course you have to build and install the perl version you
> fancy yourself - and you have to use the correct version of bioperl.
> > > > >>>
> > > > >>> There are quite a few perl installation management tools and
> ways to install CPAN modules available, like
> > > > >>>
> > > > >>> • perlbrew http://perlbrew.pl/
> > > > >>> • cpanm http://www.cpan.org/modules/INSTALL.html
> > > > >>>
> > > > >>> Once you've built your main perl version, you can use Tasks -
> the successor to Bundle::, l to build a list of recommended modules -
> > > > >>> example tasks are here :
> > > > >>>
> > > > >>> Task::Moose -
> http://search.cpan.org/~doy/Task-Moose-0.03/lib/Task/Moose.pm
> > > > >>> Task::Catalyst -
> http://search.cpan.org/~bobtfish/Task-Catalyst-4.02/lib/Task/Catalyst.pm
> > > > >>> Task::Kensho -
> http://search.cpan.org/~ether/Task-Kensho-0.33/lib/Task/Kensho.pm
> > > > >>> Task::Jenkins …
> > > > >>>
> > > > >>> Maybe one day we even have a Task::Ensembl on CPAN ? Or even
> Ensembl itself ?
> > > > >>>
> > > > >>>
> > > > >>> That's my 5 cents worth of insights,
> > > > >>>
> > > > >>> Jan Vogel
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>>
> > > > >>> On Jan 9, 2014, at 10:16 AM, Jennifer Staab <jstaab at cs.unc.edu>
> wrote:
> > > > >>>
> > > > >>>> Hi Andy, I work with Ed and have been following the thread
> about the upgrade from Perl 5.8 to 5.14 with Ensembl version 75.
> > > > >>>>
> > > > >>>> We are running Ubuntu 11.10 (Oneiric) which upgrades to Perl
> 5.12.4 using standard Ubuntu methods. We use the Perl Ensembl API,
> regularly. Since 11.10 is no longer supported by Ubuntu, we would have to
> force the upgrade to 5.14 – via CPAN. My issue with this is that it's
> possible there are incompatibilities with Perl 5.14 and Ubuntu 11.10 that
> exist and won’t be fixed because 11.10 is no longer supported.
> > > > >>>>
> > > > >>>> I believe a staged upgrade to 5.10 would solve things because
> what we use now (5.12.4) should be compatible (?) with any changes
> regarding upgrade to Perl 5.10. This staged upgrade would give us (and
> others) time to do necessary upgrades to OS (like 11.10 to 12.04) at a less
> than rushed pace.
> > > > >>>>
> > > > >>>> Thanks,
> > > > >>>>
> > > > >>>> -Jennifer
> > > > >>>>
> > > > >>>> Sent from my Verizon Wireless 4G LTE DROID
> > > > >>>>
> > > > >>>>
> > > > >>>> Andy Yates <ayates at ebi.ac.uk> wrote:
> > > > >>>>
> > > > >>>> Hi Ed,
> > > > >>>>
> > > > >>>> Thanks for the response as this is useful information to know.
> So I have a number of questions:
> > > > >>>>
> > > > >>>> 1). What kind of user are you primarily? Are you a Perl API,
> website or tool (VEP) user?
> > > > >>>> 2). Would a two release delay in upgrade (75 & 76) give
> adequate reaction time?
> > > > >>>> 3). AFAIK Ubuntu Lucid ships with Perl 5.10.1. Would you be
> more comfortable with a staged migration. This could be useful for us as it
> would minimise the amount of changes we would have to back-out and minimise
> the chances of APIs breaking
> > > > >>>>
> > > > >>>> We do want to move away from perl 5.8 as quickly as possible
> since we do not maintain a Perl 5.8 distribution internally. It is not
> possible for us to detect when we make 5.8+ only changes to the API ATMO*.
> > > > >>>>
> > > > >>>> Cheers,
> > > > >>>>
> > > > >>>> Andy
> > > > >>>>
> > > > >>>> * Now our projects are hosted at GitHub we are looking into
> using TravisCI. This can test multiple Perl versions. However not all areas
> of the project will have this level of continuous integration
> > > > >>>>
> > > > >>>> ------------
> > > > >>>> Andrew Yates - Ensembl Support Coordinator
> > > > >>>> European Bioinformatics Institute (EMBL-EBI)
> > > > >>>> European Molecular Biology Laboratory
> > > > >>>> Wellcome Trust Genome Campus
> > > > >>>> Hinxton
> > > > >>>> Cambridge CB10 1SD
> > > > >>>> Tel: +44-(0)1223-492538
> > > > >>>> Fax: +44-(0)1223-494468
> > > > >>>> http://www.ensembl.org/
> > > > >>>>
> > > > >>>> On 9 Jan 2014, at 02:39, Ed Gray <gray_ed at hotmail.com> wrote:
> > > > >>>>
> > > > >>>> > Hi Andy,
> > > > >>>> >
> > > > >>>> > Frankly for many of us, we have smallish teams that need a
> bit more time to react to discontinuing support for the old perl. Many of
> us are still on Ubuntu 11.
> > > > >>>> >
> > > > >>>> > Ed
> > > > >>>> >
> > > > >>>> >
> > > > >>>> > > From: ap5 at sanger.ac.uk
> > > > >>>> > > Date: Wed, 8 Jan 2014 13:30:18 +0000
> > > > >>>> > > To: dev at ensembl.org
> > > > >>>> > > Subject: Re: [ensembl-dev] Perl Version Upgrade
> > > > >>>> > >
> > > > >>>> > > Not as far as I know - the new BLAST code doesn't use it,
> and that was our only outstanding dependency. We'll confirm that, though,
> when we're sure that the new interface will make it into 75.
> > > > >>>> > >
> > > > >>>> > > Cheers
> > > > >>>> > >
> > > > >>>> > > Anne
> > > > >>>> > >
> > > > >>>> > >
> > > > >>>> > > On 8 Jan 2014, at 13:27, Hans-Rudolf Hotz <hrh at fmi.ch>
> wrote:
> > > > >>>> > >
> > > > >>>> > > > Hi Andy
> > > > >>>> > > >
> > > > >>>> > > >
> > > > >>>> > > > Thank you very much for the 'heads-up'
> > > > >>>> > > >
> > > > >>>> > > > Just a quick question in order to double check: Ensembl
> 75 will still require the old BioPerl version (i.e. BioPerl 1.2.3) ?
> > > > >>>> > > >
> > > > >>>> > > > Regards, Hans
> > > > >>>> > > >
> > > > >>>> > > >
> > > > >>>> > > >
> > > > >>>> > > > On 01/08/2014 03:33 AM, dev-request at ensembl.org wrote:
> > > > >>>> > > >
> > > > >>>> > > >>
> > > > >>>> > > >> Message: 1
> > > > >>>> > > >> Date: Tue, 7 Jan 2014 16:14:39 +0000
> > > > >>>> > > >> From: Andy Yates <ayates at ebi.ac.uk>
> > > > >>>> > > >> Subject: [ensembl-dev] Perl Version Upgrade
> > > > >>>> > > >> To: Ensembl developers list <dev at ensembl.org>
> > > > >>>> > > >> Message-ID: <
> 8918159B-5D53-435F-8DFD-EB235DC877AB at ebi.ac.uk>
> > > > >>>> > > >> Content-Type: text/plain; charset=us-ascii
> > > > >>>> > > >>
> > > > >>>> > > >> Dear all,
> > > > >>>> > > >>
> > > > >>>> > > >> In 2013 the Ensembl team spent a significant amount of
> time upgrading our internal Perl version from 5.8 to 5.14 (totalling a 9
> year development gap). This was in part motivated by the improved runtime
> and memory consumption seen in later versions of Perl especially in the
> 5.14 development tree. We were also motivated by some new language
> constructs only available with later versions of Perl (smart match
> operators, non-destructive regular expressions, defined OR operators).
> > > > >>>> > > >>
> > > > >>>> > > >> From release 75 we wish to increase the minimal Perl
> version for Ensembl from 5.8 to 5.14.
> > > > >>>> > > >>
> > > > >>>> > > >> Many OS ship with compatible versions of Perl out of the
> box; to check what version of Perl you are currently running you should
> execute the following from your command line (anything with 5.14 or above
> is great):
> > > > >>>> > > >>
> > > > >>>> > > >> $ perl -v
> > > > >>>> > > >> This is perl 5, version 14, subversion 4 (v5.14.4) built
> for darwin-thread-multi-2level
> > > > >>>> > > >>
> > > > >>>> > > >> Should you have any questions or concerns about this
> move please get in touch ASAP either here on dev or via helpdesk.
> > > > >>>> > > >>
> > > > >>>> > > >> All the best,
> > > > >>>> > > >>
> > > > >>>> > > >> Andy
> > > > >>>> > > >>
> > > > >>>> > > >> ------------
> > > > >>>> > > >> Andrew Yates - Ensembl Support Coordinator
> > > > >>>> > > >> European Bioinformatics Institute (EMBL-EBI)
> > > > >>>> > > >> European Molecular Biology Laboratory
> > > > >>>> > > >> Wellcome Trust Genome Campus
> > > > >>>> > > >> Hinxton
> > > > >>>> > > >> Cambridge CB10 1SD
> > > > >>>> > > >> Tel: +44-(0)1223-492538
> > > > >>>> > > >> Fax: +44-(0)1223-494468
> > > > >>>> > > >> http://www.ensembl.org/
> > > > >>>> > > >>
> > > > >>>> > > >>
> > > > >>>> > > >>
> > > > >>>> > > >
> > > > >>>> > > > --
> > > > >>>> > > >
> > > > >>>> > > >
> > > > >>>> > > >
> > > > >>>> > > > Hans-Rudolf Hotz, PhD
> > > > >>>> > > > Bioinformatics Support
> > > > >>>> > > >
> > > > >>>> > > > Friedrich Miescher Institute for Biomedical Research
> > > > >>>> > > > Maulbeerstrasse 66
> > > > >>>> > > > 4058 Basel/Switzerland
> > > > >>>> > > >
> > > > >>>> > > > _______________________________________________
> > > > >>>> > > > Dev mailing list Dev at ensembl.org
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> > > > >>>> > >
> > > > >>>> > > Anne Parker
> > > > >>>> > > Ensembl Web Production Manager
> > > > >>>> > > http://www.ensembl.org
> > > > >>>> > >
> > > > >>>> > >
> > > > >>>> > >
> > > > >>>> > >
> > > > >>>> > > _______________________________________________
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-- 

William Spooner, PhD
CTO and Founder
Eagle Genomics Ltd, Breathing Life into Big Data
Babraham Research Campus, Cambridge CB22 3AT, UK
T: +44 (0)1223 497371 | M: +44 (0)7779 663045
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