Pipeline source code and environment

Checkout codebases from Github

Pipeline config

  git clone https://github.com/imperial-genomics-facility/igf-pipelines.git

Python library for IGF pipelines

  git clone https://github.com/imperial-genomics-facility/data-management-python.git

Ensembl ehive pipeline

  git clone https://github.com/Ensembl/ensembl-hive.git

PBSpro meadow interface for Ensembl ehive

  git clone https://github.com/Ensembl/ensembl-hive-pbspro.git

Use system perl or install specific perl version using perlbrew. Check for required perl modules after installation using the following command

  perl -e 'use DBI;use DBD::mysql;use DBD::SQLite;IPC::Run;'

Install the missing packages using cpan (for system perl) or cpanm (for perlbrew) if they are not already present.

  cpan install DBI
  cpan install DBD::mysql
  cpan install DBD::SQLite
  cpan install IPC::Run

Setup environment using conda

Download and setup miniconda

  wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
  bash Miniconda3-latest-Linux-x86_64.sh

Create an conda environment using the configuration file

  conda env create --name pipeline-env --file igf-pipelines/environment.yaml

Activate the conda environment using the following command

  source activate pipeline-env

Deactivate conda env

  source deactivate

Create a new file, e.g. env.sh and

Add PERL5LIB variables

  export PERL5LIB=/path/ensembl-hive/modules:/path/ensembl-hive-pbspro/modules:/path/igf-pipelines/modules:${PERL5LIB}

Add PATH variable

  export PATH=/path/ensembl-hive/scripts:${PATH}

Add PYTHONPATH variables

  export PYTHONPATH=/path/data-management-python/:/path/ensembl-hive/wrappers/python3:${PYTHONPATH}

Then activate environment for pipeline using source env.sh command.