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

[Shane McCoy]

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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