Monday, October 21, 2013

Installing Ensembl API

Ensembl has a cool sets of sub routines very useful. For some people installing and testing is just very easy but for some it may be very difficult especially when you are setting up a new server. You just get the API from where step by step instructions are given.

Many times running /ensembl/misc-scripts/ tell you what is the problem. In our instance it kep complaining about installation of DBI even though DBI was very much there. Looking into the complaining part:

101 eval {
102   require DBI;
103   require DBD::mysql;
104   require Bio::Perl;
105   require Bio::EnsEMBL::Registry;
106   require Bio::EnsEMBL::ApiVersion;
107   require Bio::EnsEMBL::LookUp if $ensembl_genomes;
108   $api_version = Bio::EnsEMBL::ApiVersion::software_version();

I realized that DBD::mysql is required and is not available in my machine. Then login as root and type cpan at the command mode, then do an 'install DBD::mysql' exits with lot of error. Tracing back it says can't find mysql.h. I looked for the source and never found them since I had only done a yum install mysql-server. In this case, you first have to do a yum install mysql-devel. Then go to cpan and do force install DBD::mysql. So, probably it will install.

Set Path for Ensembl:

As written in the document, set paths for ensembl packages as below:

export PERL5LIB=$PERL5LIB:/home/sutripa/ensembl/modules
export PERL5LIB=$PERL5LIB:/home/sutripa/ensembl-compara/modules
export PERL5LIB=$PERL5LIB:/home/sutripa/ensembl-functgenomic/modules
export PERL5LIB=$PERL5LIB:/home/sutripa/ensembl-variation/modules

export PERL5LIB=$PERL5LIB:/home/sutripa/ensembl-tools/

Then go to:

ensembl/misc-scripts and run  ./ and see if you get a message like this:
Installation is good. Connection to Ensembl works and you can query the human co
re database

Then you are good to go....

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