[ensembl-dev] Perl Version Upgrade

Andy Yates ayates at ebi.ac.uk
Mon Jan 13 20:56:19 GMT 2014


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
> > > >>>> > > > 
> > > >>>> > > > _______________________________________________
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> > > >>>> > > 
> > > >>>> > > Anne Parker
> > > >>>> > > Ensembl Web Production Manager
> > > >>>> > > http://www.ensembl.org
> > > >>>> > > 
> > > >>>> > > 
> > > >>>> > > 
> > > >>>> > > 
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