conda environment has still dependencies for external package mwTools

[webermarcolivier]

the script index_genome_files_bowtie2.py imports functions from the mwTools package, which is not included in the conda environment. External user could not run correctly the pipeline because of this missing dependencies.
Two solutions

1. For the moment, include functions code directly in the index_genome_files_bowtie2.py script.
2. Later, refactor the mwTools to a full python package and install it in the conda environment.

[webermarcolivier]

Including code of external function in the index_genome_files_bowtie2.py script is a bad idea, I reverted the commit.

For the moment the external python packages mwTools is loaded by adding its path to the PYTHON_PATH. This, together with loading the DRMAA library, is still done in the load_dependencies.sh script, which needs to be loaded by external user before calling the pipeline.

In the future, I will refactor the mwTools package to install it in the conda environment.