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Just an update on this; I contacted Chris D. and Bundle::BioPerl is now on github:
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<div class=""><a href="https://github.com/bioperl/Bundle-BioPerl" class="">https://github.com/bioperl/Bundle-BioPerl</a></div>
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<div class="">I’ll work on pushing a new release up to CPAN, will post back when that is done.</div>
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<div class="">chris (f)</div>
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<div class="">On Jan 14, 2015, at 2:14 PM, Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" class="">cjfields@illinois.edu</a>> wrote:</div>
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<div class="">Bundle::BioPerl is out of date.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.</div>
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<div class="">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.</div>
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<div class="">The github master version should technically be ‘1.007000_001’ or similar, not ‘1.006925’. I’ll have a look at that.</div>
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<div class="">chris</div>
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<div class="">On Jan 13, 2015, at 5:23 PM, Shane McCoy <<a href="mailto:shanemccoypdx@gmail.com" class="">shanemccoypdx@gmail.com</a>> wrote:</div>
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<div dir="ltr" class="">Hello!
<div class="">Not too familiar w/ Bioperl and want to make sure i've properly installed on my VM ubuntu 14.4 server w/ git. </div>
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<div class=""><a href="http://www.bioperl.org/wiki/BioPerl_Dependencies" class="">http://www.bioperl.org/wiki/BioPerl_Dependencies</a></div>
<div class=""><a href="http://www.bioperl.org/wiki/Using_Git" class="">http://www.bioperl.org/wiki/Using_Git</a></div>
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<div class="">sudo apt-get update</div>
<div class="">sudo apt-get upgrade</div>
<div class="">sudo apt-get check</div>
<div class="">sudo apt-get autoclean</div>
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<div class="">sudo apt-get install build-essential git gcc</div>
<div class="">sudo apt-get install libexpat1 expat</div>
<div class="">sudo apt-get install libgd-dev (unable to locate libgd recommended on
<a href="http://gmod.org/wiki/BioPerl" class="">gmod.org/wiki/BioPerl</a> Dependencies Outside perl)</div>
<div class="">sudo apt-get install libssl-dev</div>
<div class="">sudo apt-get install libpq-dev</div>
<div class="">sudo apt-get install libdb-dev libperl-dev</div>
<div class="">sudo apt-get install libgd-gd2-perl</div>
<div class="">sudo apt-get install libxml2</div>
<div class="">sudo apt-get install libxml2-dev</div>
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<div class="">Installed local::lib manually for perl modules. Set environment path </div>
<div class="">echo '[ $SHLVL -eq 1 ] && eval "$(perl -I$HOME/perl5/lib/perl5 -Mlocal::lib)"' >>~/.bashrc</div>
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<div class="">cpan> install Bundle::CPAN (archive::zip failed? pff!) </div>
<div class="">cpan> install Bundle::BioPerl</div>
<div class="">Failed during this command:</div>
<div class=""> LDS/AcePerl-1.92.tar.gz : make_test NO</div>
<div class=""> CJFIELDS/Bio-ASN1-EntrezGene-1.70.tar.gz : make_test NO</div>
<div class=""> CAPTTOFU/DBD-mysql-4.029.tar.gz : writemakefile NO '/usr/bin/perl Makefile.PL </div>
<div class="">and several more. missing packages etc and successfully installed except the above 3. Don't think i need those.</div>
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<div class="">sudo apt-get install libgd-gd2-perl</div>
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git clone <a href="https://github.com/bioperl/bioperl-live.git" class="">
https://github.com/bioperl/bioperl-live.git</a>
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<div class="">cd bioperl-live
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<div class="">perl Build.PL
--fails - needs more modules</div>
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<div class="">Configuring C/CJ/CJFIELDS/BioPerl-1.6.924.tar.gz with Build.PL</div>
<div class="">Checking prerequisites...</div>
<div class=""> recommends:</div>
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<div class="">Algorithm::Munkres </div>
<div class="">Array::Compare </div>
<div class="">Bio::Phylo </div>
<div class="">Convert::Binary::C </div>
<div class="">GraphViz</div>
<div class="">HTML::TableExtract is not installed</div>
<div class="">PostScript::TextBlock is not installed</div>
<div class="">SOAP::Lite </div>
<div class="">Net::SSLeay Crypt::SSLeay IO::Socket::SSL</div>
<div class="">Sort::Naturally </div>
<div class="">XML::LibXML </div>
<div class="">DBD::Pg </div>
<div class="">DBD::SQLite</div>
<div class="">(all above installed via CPAN)</div>
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<div class="">Checking optional features...</div>
<div class="">EntrezGene............disabled</div>
<div class=""> requires:</div>
<div class=""> ! Bio::ASN1::EntrezGene is not installed</div>
<div class=""> - starts installing bioperl </div>
<div class="">i let it run and it installed Bioperl fine via CPAN. build OK. </div>
<div class="">Installed bio::asn1::entrezgene & bio::root::build</div>
<div class="">perl Build.PL</div>
<div class="">now needs Inline::C...</div>
<div class="">cpan>install Inline::C</div>
<div class=""> cd bioperl-live </div>
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perl Build.PL
-- fails. missing Manifest?</div>
<div class="">Build manifest</div>
<div class="">perl Build.PL --still fails</div>
<div class="">perl Build -- works</div>
<div class="">./Build test
--PASS</div>
<div class="">sudo ./Build install </div>
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<div class="">Installed / passed tests OK. </div>
<div class="">Added;</div>
<div class="">export PERL5LIB="$HOME/bioperl-live:$PERL5LIB"</div>
<div class="">to .bashrc</div>
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<div class="">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? </div>
<div class="">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. </div>
<div class="">Ok, thanks for your time! Just want to make sure i'm doing this correctly. </div>
<div class="">Shane</div>
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