Bugfixes for Python 3

• fixes for building the docs
• pipeline_peakcalling: changed default blacklist path; #345
• pipeline_peakcalling: bedGraphToBigWig in new environment requires sorted input; #346
• pipeline_peakcalling: debugging for python 3 in peakcalling notebook reports and changing default format to python 3; #347
• added scripts to help find R and Python dependencies: scripts/cgat_deps_R.sh, scripts/cgat_deps_python.sh
• pipeline_peakcalling: added an additional plotting function to generate summary plots after IDR; #348
• pipeline_peakcalling: redirected optimal peaks and conservative peaks to filtered IDR output; #349
• pipeline_rnaseqqc: added functions to check the strandedness of the library, which is required as an input for various mappers; #351
• remove unused imports with autoflakes; #354
• bugfix the way bowtie2 index folder is configured in pipeline_mapping; #356 and #361
• bowtie should not use the quite option so multiqc reports properly; #357
• pipeline_peakcalling: minor bugfix; #358
• pipeline_peakcalling: update to work with sicer in a Python 2 environment ; #359
• added cgatflow command; #360
• updated documentation and moved unused code to obsolete folder; #362
• updated installation; #363 ; #367
• pipeline_peakcalling: update the way IDR is called so it is included as a conda dependency ; #364