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

[Shane McCoy]

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  Bundle::BioPerl is out of date.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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