Install Ensembl API and BioPerl 1.2.3 on Your System
By Güngör Budak
- 2 minutes read - 226 wordsI’m going to work on a project that requires lots of queries on Ensembl databases so I wanted to install Ensembl API to begin with. Since it’s programmed in Perl, I will be using Perl in this project.
There is a nice tutorial on Ensembl website for API installation. Here I will describe some steps.
1. Download the API and BioPerl
Go to Ensembl FTP ftp://ftp.ensembl.org/pub/ and download “ensembl-api.tar.gz” or click here
Go to BioPerl downloads page http://bioperl.org/DIST/old_releases/ download stable 1.6.1 1.2.3 version (in tar.gz)
2. Place your in a source directory
On Ubuntu, you can use the code below to generate your source folder, extract the downloads and then move the content to your source folder
1mkdir ~/src
2tar xvfz ensembl-api.tar.gz
3mv ensembl ~/src/ensembl
4mv ensembl-compara ~/src/ensembl-compara
5mv ensembl-functgenomics ~/src/ensembl-functgenomics
6mv ensembl-tools ~/src/ensembl-tools
7mv ensembl-variation ~/src/ensembl-variation
8tar xvfz BioPerl-1.2.3.tar.gz
9mv BioPerl-1.2.3 ~/src/bioperl-1.2.3
3. Set your environment variables so tat Perl 5 can find the source directory and files inside
1gedit ~/.bashrc
Add following lines to at the end of .bashrc;
1PERL5LIB=${HOME}/src/bioperl-1.2.3
2PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl/modules
3PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-compara/modules
4PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-variation/modules
5PERL5LIB=${PERL5LIB}:${HOME}/src/ensembl-functgenomics/modules
6export PERL5LIB
Then;
1source ~/.bashrc
4. Check if the installation is successful
1perl ~/src/ensembl/misc-scripts/ping_ensembl.pl
If you get “Installation is good. Connection to Ensembl works and you can query the human core database”, it’s done.
For more information and the steps in installation on Mac and Windows see the original tutorial.