dev

I will explain how I set up my env to test my changes in bcbio code.

Clone the repository

git clone [email protected]:user/bcbio-nextgen

You can run this command to install only scripts:

$STABLE/anaconda/bin/python2.7 bcbio_nextgen_install.py /path_to_bcbio --isolate -u development

Now you have to set up your env vars to your stable bcbio installation that you know it works properly:

export PATH=/path_to_bcbio/anaconda/bin:$PATH2STABLE/bcbio_nextgen/anaconda/bin/:$PATH
#export LD_LIBRARY_PATH=$PATH2STABLE/bcbio_nextgen/lib:$LD_LIBRARY_PATH
#export PERL5LIB=$PATH2STABLE/bcbio_nextgen/lib/perl5:$PATH2STABLE/bcbio_nextgen/lib/perl5/site_perl

Last you need to link your genome, galaxy, Cellar, manifest, gemini and gemini_data to your dev path: /path_to_bcbio/

Now you can use all third party tools from your stable bcbio, but with your dev code.

How to change the code?

• correct way

 path_to_bcbio/anaconda/bin/python2.7 python setup.py develop

From now on, any change in the code in your repository will have effect in the analysis you run.