bugfix cgat CLI added scripts to help find R and Python dependencies: scripts/cgat_deps_R.sh, scripts/cgat_deps_python.sh modified install script to use conda environment files instead of conda meta-packages; https://github.com/CGATOxford/cgat/pull/343 update test_style.py to reflect new repository structure; https://github.com/CGATOxford/cgat/pull/345 update test_import.py to reflect new repository structure; https://github.com/CGATOxford/cgat/commit/decc5ec0e93b4d2c05b6fa3793b5a73caf1fa8b9 added script to perform Gene Set Enrichment Analysis; https://github.com/CGATOxford/cgat/pull/344 updated scripts to work with Python 3.6; https://github.com/CGATOxford/cgat/pull/346 bugfix bed2bed script; https://github.com/CGATOxford/cgat/pull/349; https://github.com/CGATOxford/cgat/issues/347 bugfix GTF.py module file; https://github.com/CGATOxford/cgat/issues/350 various bugfixes for Python 3 problems when running pipeline_annotations in python 3, plus a modification of the new "assembly report" section to allow genomes without a standard assembly report (e.g. yeast) to be processed; https://github.com/CGATOxford/cgat/pull/348 refactor CGAT/PipelineGWAS.py to CGAT/GWAS.py; https://github.com/CGATOxford/cgat/pull/354 removed unused imports with autoflakes; https://github.com/CGATOxford/cgat/pull/355 removed basestr, use str instead in Python 3; https://github.com/CGATOxford/cgat/pull/359 added test for csv2db; https://github.com/CGATOxford/cgat/pull/360 fixed rename_transcripts test for gtf2gtf.py; https://github.com/CGATOxford/cgat/pull/361 updated installation; https://github.com/CGATOxford/cgat/pull/364 ; https://github.com/CGATOxford/cgat/pull/373 updated documentation; https://github.com/CGATOxford/cgat/pull/365 ; https://github.com/CGATOxford/cgat/pull/367 replaced bx.bbi.bigwig_file with pyBigWig ; https://github.com/CGATOxford/cgat/pull/369 updated Expression.py to iterate over pandas dataframe; https://github.com/CGATOxford/cgat/pull/370 updated Expression.py to work with DESeq2 > 1.16 ; https://github.com/CGATOxford/cgat/pull/371 moved bed_vs_bed.py to obsolete ; https://github.com/CGATOxford/cgat/pull/372