Re: Properly installing Bioperl - Ubuntu - Git

Hi Chris,

Thanks for looking into this! I am also experiencing the same problem encountered by Shane.

Thanks,

Lili

Liliana Cano, PhD.
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Dept. Plant Pathology
North Carolina State University
Raleigh, NC 27695, USA.
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On Jan 16, 2015, at 11:30 AM, Shane McCoy <[email protected]> wrote:

> Thanks Chris!
> appreciate you looking into this
> shane
> 
> On Thu, Jan 15, 2015 at 11:32 AM, Fields, Christopher J <[email protected]> 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 <[email protected]> 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 Bundle::BioPerl is out of date.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 <[email protected]> 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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>> 
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