Gwip

The tutorial script was updated:
* Checks binaries in the system path before downloading them.
* Updated link to download Plink.

This release includes the following changes:
- Compatibility with _statsmodels_ version 0.8.0.
- Conda package for Python 3.6.

This release includes the following changes:
- When launching the pipeline, using `--chrom autosomes` will now launch the analysis on all autosomes (from chromosomes 1 to 22).
- The tutorial script (`genipe-tutorial`) now performs the analysis on the autosomes.

Changes to the **main imputation pipeline** include:
- Can now impute only a subset of chromosomes (the `--chrom` option).
- Possibility to further customize SHAPEIT (the `--shapeit-extra` option).
- Possibility to further customize IMPUTE2 (the `--impute2-extra` option).
- Chromosome X (both pseudo- and non-pseudo-autosomal regions) are now imputable.

Changes to the **statistical tool** include:
- Mixed linear model is now optimized to significantly reduce computation time.
- Better handling of categorical variables in survival analysis (CoxPH) (the `--categorical` option).
- Linear analysis now returns the adjusted r-squared value.

Changes to the **extraction tool** include:
- Addition of the _LGEN_ output format (the `--long` option, available for the `calls` and `dosage` format).
- Addition of the _BED_ output format (the `--format bed` option).

_The compatibility with Python 3.3 was removed (since `pandas` versions are too old in anaconda for this version)._

Changes include:
- A standalone script that downloads reference files, genotype files and binaries to help the user execute the main pipeline tutorial (be sure to check the binaries licences (see [here](http://pgxcentre.github.io/genipe/tutorials/tutorial_genipe.htmlpreparing-the-data) for more information).
- Better documentation.

Changes include:
- Automatic report
- creates a bar plot instead of a pie chart for better frequency comparison
- minor amelioration in the template (for file names)
- option (`--report-background`) to change the content of the background section
- `impute2-extractor`
- possible to only index impute2 files using `--index`
- when extracting in impute2 format, the companion files are also processed
- corrected some tests that failed depending of system used