[Bioperl-l] Properly installing Bioperl - Ubuntu - Git

Sat Jan 17 17:40:23 UTC 2015

Hey Chris!
Thanks for the update. I don't believe i'm using the master, i used: git
clone git://github.com/bioperl/bioperl-live.git
So the version is correct then? 1.006924 for the above git clone.
thanks for your time!
shane

On Fri, Jan 16, 2015 at 3:30 PM, Fields, Christopher J <
cjfields at illinois.edu> wrote:

>  I’ve uploaded a new version of Bundle::BioPerl to CPAN (this removes Ace
> and Bio::ASN1::EntrezGene).
>
>  One key thing: the ‘master’ branch on github is *not* the branch you
> want to check out from if you want stable code; you need the ‘v1.6.x’
> branch.  We’re splitting out repositories from the main distribution (about
> 4 or so now), so if you try to run a typical installation it may not work
> as Bio::Root will be missing.
>
>  chris
>
>  On Jan 16, 2015, at 10:42 AM, Liliana Maria Cano Mogrovejo <
> lcanomo at ncsu.edu> wrote:
>
>  Hi Chris,
>
>  Thanks for looking into this! I am also experiencing the same problem
> encountered by Shane.
>
>  Thanks,
>
>  Lili
>
>      Liliana Cano, PhD.
>  Postdoctoral Research Associate
>  Dept. Plant Pathology
>  North Carolina State University
>  Raleigh, NC 27695, USA.
>  Email: lcanomo at ncsu.edu
>  Phone: +1-919-513-1280
>  Mobile: +1-919-703-6147
>
>  https://twitter.com/ConchitaCano
> http://plantpathology.ces.ncsu.edu/profile/liliana-cano/
>
>  On Jan 16, 2015, at 11:30 AM, Shane McCoy <shanemccoypdx at gmail.com>
> wrote:
>
>  Thanks Chris!
> appreciate you looking into this
> shane
>
> On Thu, Jan 15, 2015 at 11:32 AM, Fields, Christopher J <
> cjfields at illinois.edu> wrote:
>
>> Just an update on this; I contacted Chris D. and Bundle::BioPerl is now
>> on github:
>>
>>  https://github.com/bioperl/Bundle-BioPerl
>>
>>  I’ll work on pushing a new release up to CPAN, will post back when that
>> is done.
>>
>>  chris (f)
>>
>>  On Jan 14, 2015, at 2:14 PM, Fields, Christopher J <
>> cjfields at illinois.edu> wrote:
>>
>>  Bundle::BioPerl is out of date.  I’ll have to check in with Chris
>> Dagdigian to see if we can update that, as it’s not on github.
>>
>>  Unless you are using NCBI and the ‘gene’ database, you won’t need
>> Bio::ASN1::EntrezGene.  The latest CPAN releases for both should still
>> resolve the circular dependency though; not sure why you are running into
>> this problem.
>>
>>  The github master version should technically be ‘1.007000_001’ or
>> similar, not ‘1.006925’.   I’ll have a look at that.
>>
>>  chris
>>
>>  On Jan 13, 2015, at 5:23 PM, Shane McCoy <shanemccoypdx at gmail.com>
>> wrote:
>>
>>  Hello!
>> Not too familiar w/ Bioperl and want to make sure i've properly installed
>> on my VM ubuntu 14.4 server w/ git.
>>  http://www.bioperl.org/wiki/BioPerl_Dependencies
>> http://www.bioperl.org/wiki/Using_Git
>>
>>  sudo apt-get update
>> sudo apt-get upgrade
>> sudo apt-get check
>> sudo apt-get autoclean
>>
>>  sudo apt-get install build-essential git gcc
>> sudo apt-get install libexpat1 expat
>> sudo apt-get install libgd-dev  (unable to locate libgd recommended on
>> gmod.org/wiki/BioPerl Dependencies Outside perl)
>> sudo apt-get install libssl-dev
>> sudo apt-get install libpq-dev
>> sudo apt-get install libdb-dev libperl-dev
>> sudo apt-get install libgd-gd2-perl
>> sudo apt-get install libxml2
>> sudo apt-get install libxml2-dev
>>
>>  Installed local::lib manually for perl modules. Set environment path
>> echo '[ $SHLVL -eq 1 ] && eval "$(perl -I$HOME/perl5/lib/perl5
>> -Mlocal::lib)"' >>~/.bashrc
>>
>>  cpan> install Bundle::CPAN (archive::zip failed? pff!)
>> cpan> install Bundle::BioPerl
>> Failed during this command:
>>  LDS/AcePerl-1.92.tar.gz                      : make_test NO
>>  CJFIELDS/Bio-ASN1-EntrezGene-1.70.tar.gz     : make_test NO
>>  CAPTTOFU/DBD-mysql-4.029.tar.gz              : writemakefile NO
>> '/usr/bin/perl Makefile.PL
>> and several more. missing packages etc and successfully installed except
>> the above 3. Don't think i need those.
>>
>>  sudo apt-get install libgd-gd2-perl
>>
>>  git clone https://github.com/bioperl/bioperl-live.git
>> cd bioperl-live
>> perl Build.PL --fails - needs more modules
>>
>>
>>  Configuring C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz with Build.PL
>> Checking prerequisites...
>>   recommends:
>>
>>  Algorithm::Munkres
>> Array::Compare
>> Bio::Phylo
>> Convert::Binary::C
>> GraphViz
>> HTML::TableExtract is not installed
>> PostScript::TextBlock is not installed
>> SOAP::Lite
>> Net::SSLeay Crypt::SSLeay IO::Socket::SSL
>> Sort::Naturally
>> XML::LibXML
>> DBD::Pg
>> DBD::SQLite
>> (all above installed via CPAN)
>>
>>  Checking optional features...
>> EntrezGene............disabled
>>   requires:
>>     ! Bio::ASN1::EntrezGene is not installed
>>  - starts installing bioperl
>> i let it run and it installed Bioperl fine via CPAN.  build OK.
>> Installed bio::asn1::entrezgene & bio::root::build
>> perl Build.PL
>> now needs Inline::C...
>> cpan>install Inline::C
>>  cd bioperl-live
>>  perl Build.PL -- fails. missing Manifest?
>> Build manifest
>> perl Build.PL --still fails
>> perl Build -- works
>> ./Build test --PASS
>> sudo ./Build install
>>
>>  Installed / passed tests OK.
>> Added;
>> export PERL5LIB="$HOME/bioperl-live:$PERL5LIB"
>> to .bashrc
>>
>>  So i've installed via CPAN which i didn't really want, but couldn't run
>> Build.PL w/o prereq Bio::ASN1::EntrezGene which starts installing bioperl.
>> What should i have done differently?
>> i still did Build w/ Git clone, but when i check Version i get 1.006924.
>> I thought the bioperl-live version was 1.006925? i set the environment
>> variable in bashrc for bioperl-live.
>> Ok, thanks for your time! Just want to make sure i'm doing this
>> correctly.
>> Shane
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