[Bioperl-l] Installing Bio-perl on dreamhost via CPAN

Chris Fields cjfields at illinois.edu
Fri Nov 20 15:40:24 EST 2009


BioPerl is pure perl.  If you believe all dependencies are installed, just unpack the dist to a specific directory and point PERL5LIB at it (for bash):

export PERL5LIB=/home/USER/bioperl/bioperl-live

Note that if you plan on doing the same for other bioperl-related modules (ex: bioperl-db) you'll need to add 'lib' to it, as they use a generic Module::Build now.

export PERL5LIB=/home/USER/bioperl/bioperl-db/lib

You can also add a 'use lib' directive in your scripts as well.  More at the following link:

http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#USING_MODULES_NOT_INSTALLED_IN_THE_STANDARD_LOCATION

chris

On Nov 20, 2009, at 2:23 PM, Chu, Roy wrote:

> "sounds very much like you process was killed for prolonged execution
> time, or memory usage. We have a daemon in place that monitors for
> processes that take up too much of a shared web server's resources, and
> this may have kicked in (and often does when trying to install packages
> on a shared server)."
> 
> This was the explanation they had.  Regarding asking their admins to
> install, it seems is a "they'll try to get to it but don't hold your
> breath situation."
> 
> Hmmm, I tried some other attempts, installing 1.4.0 posed no problems.
> I'm not a perl guru, so I tried to increase the build cache size from
> the default, 10 MB, hoping that that may be the problem--can't imagine
> how though, since I can't imagine how big the whole package version
> can differ by (though honestly, I haven't checked).
> Whenever I try to install 1.6.1, it runs into a problem I guess after
> the 'make' step and lists the
> modules--BioPerl-1.6.0/t/Variation/SeqDiff.t
> BioPerl-1.6.0/t/Variation/SNP.t
> BioPerl-1.6.0/t/Variation/Variation_IO.t
> --and typically gets killed here '> Killed'
> 
> Next, I tried 1.6.0, then I get this:
> "(I think you ran Build.PL directly, so will use CPAN to install
> prerequisites on demand)
> CPAN: Storable loaded ok (v2.12)
> Going to read '/home/$username/.cpan/Metadata'
> Killed" (everything prior works and it seems to get further along than
> when I try to install 1.6.1)
> 
> Any insight into why this may be happening would be appreciated.
> Something EQUALLY appreciated would be a recommendation of a decent
> enough hosting service where someone has had success installing
> Bio-Perl.  I'd try to set up my Mac web sharing feature and then try
> to setup the stuff locally, but I haven't yet been able to
> successfully get the port forwarding feature working properly on the
> apple airport extreme--perplexing.  Next, I might just try to install
> via the Build.pl script.
> 
> Hmm, checking the wiki, it seems I'll still be able to run remote
> blast and use the basic seq modules, although some discrepancies and
> idiosyncrasies may be expected?  Any head-ups about any false
> assumptions by me would be greatly appreciated.
> 
> Thanks in advance,
> Roy
> 
> On Fri, Nov 20, 2009 at 5:00 AM, Chris Fields <cjfields at illinois.edu> wrote:
>> 
>> On Nov 20, 2009, at 4:44 AM, Charles Plessy wrote:
>> 
>>> Le Fri, Nov 20, 2009 at 02:21:54AM -0800, Chu, Roy a écrit :
>>>> 
>>>> Does anyone use dreamhost as a web hosting service?  I'm just curious
>>>> if anyone has had any luck installing the module as their daemon seems
>>>> to kill my process whenever I try to install it.  Dreamhost tech
>>>> support attributes it to either exceeding the allocated memory cache
>>>> or exceeding the processing time.  I tried to nice the process, but
>>>> that didn't help for me.  Any luck or experience in resolving this
>>>> would be much appreciated.  I suppose my next attempt would be to try
>>>> installing it directly and hope I don't need root...
>>> 
>>> Dear Roy,
>>> 
>>> DreamHost uses Debian, so you can suggest them to install the Debian package.
>>> If you are in contact with the tech service, do not hesitate to tell them to
>>> contact me if they are interested by a backport of the 1.6.0 package. For
>>> version 1.6.1, it may be more difficult as it depends on perl 5.10.1.
>> 
>> Any reason why this is so?  We specify compatibility back to 5.6.1.
>> 
>> Alex mentioned the reliance on the specific Extutils::Manifest version.  The version requested has an important bug fix, is present on CPAN, and is backwards-compatible to 5.6.1.  It should be fairly easy to request that as a separate package.
>> 
>> A strict requirement for perl 5.10.1 doesn't make sense in that light, unless said perl maintainer can enlighten us as to why this is an issue?  This one may require a ranty blog post.
>> 
>>> PS: if you propse to install BioPerl as a feature in the Dreamhost panel, I
>>> will vote for it :)
>>> 
>>> Have a nice day,
>>> 
>>> --
>>> Charles Plessy
>>> Debian Med packaging team,
>>> http://www.debian.org/devel/debian-med
>>> Tsurumi, Kanagawa, Japan
>> 
>> chris
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>> 
> 
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