Merge branch 'tutorial_helper'

README.mkd

@@ -4,13 +4,14 @@
 
 # genipe - A Python module to perform genome-wide imputation analysis
 
-*Version 1.2.2*
-
 The `genipe` module (standing for **GEN**ome-wide **I**mputation
 **P**ipelin**E**) includes a script (named `genipe-launcher`) that
 automatically runs a genome-wide imputation pipeline using *Plink*, *shapeit*
 and *impute2*.
 
+
+## Documentation
+
 Full documentation is available at
 [http://pgxcentre.github.io/genipe/](http://pgxcentre.github.io/genipe/).
 
@@ -30,8 +31,12 @@ pip install genipe
 conda install genipe -c http://statgen.org/wp-content/uploads/Softwares/genipe
 ```
 
-The installation process should install all required dependencies, which are
-described below.
+The installation process should install all required dependencies to run the
+main imputation pipeline. Optional dependencies can also be installed manually
+in order to perform statistical analysis and data management (see below).
+
+The complete installation procedure is available in the
+[documentation](http://pgxcentre.github.io/genipe/installation.html).
 
 
 ### Dependencies
@@ -49,18 +54,19 @@ The tool requires the binaries for
 [shapeit](https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#download)
 and [impute2](https://mathgen.stats.ox.ac.uk/impute/impute_v2.html#download).
 
-A tool is provided to perform statistical analysis using the imputation results
-(linear, logistic and Cox's regressions). This tool requires the following
-Python modules:
 
-* `scipy` version 0.15.1 or latest (required by `statsmodels`)
-* `lifelines` version 0.7.0.0 and latest
-* `statsmodels` version 0.6.1 and latest
+### Optional dependencies
 
-Other packages are optional:
+In order to perform data management and statistical analysis (linear, logistic
+and Cox's regressions), `genipe` requires the following Python modules:
 
-* `Matplotlib` version 1.4.2
+* `Matplotlib` version 1.4.2 or latest
+* `scipy` version 0.15.1 or latest
+* `statsmodels` version 0.6.1 or latest
+* `lifelines` version 0.7.0 or latest
 * `Biopython` version 1.65 or latest
+* `pyfaidx` version 0.3.7 or latest
+* `drmaa` version 0.7.6 or latest
 
 Finally, the tool requires a LaTeX installation to compile the automatically
 generated report in PDF format.
@@ -106,7 +112,7 @@ usage: genipe-launcher [-h] [-v] [--debug] [--thread THREAD] --bfile PREFIX
                        [--report-background BACKGROUND]
 
 Execute the genome-wide imputation pipeline. This script is part of the
-'genipe' package, version 1.2.2.
+'genipe' package, version 1.2.3.
 
 optional arguments:
   -h, --help            show this help message and exit
@@ -217,7 +223,7 @@ usage: imputed-stats [-h] [-v] {cox,linear,logistic,mixedlm,skat} ...
 
 Performs statistical analysis on imputed data (either SKAT analysis, or
 linear, logistic or survival regression). This script is part of the 'genipe'
-package, version 1.2.2).
+package, version 1.2.3).
 
 optional arguments:
   -h, --help            show this help message and exit

docs/index.rst

@@ -58,7 +58,7 @@ Usage
                           [--report-background BACKGROUND]
 
    Execute the genome-wide imputation pipeline. This script is part of the
-   'genipe' package, version 1.2.2.
+   'genipe' package, version 1.2.3.
 
    optional arguments:
      -h, --help            show this help message and exit

docs/installation.rst

@@ -1,14 +1,7 @@
 Installation
 =============
 
-
-Quick navigation
------------------
-
-1. :ref:`install-requirements`
-2. :ref:`install-virt`
-3. :ref:`install-test`
-4. :ref:`install-update`
+.. contents:: Quick navigation
 
 
 .. _install-requirements:
@@ -32,6 +25,7 @@ management):
 * ``lifelines`` version 0.7.0 or latest
 * ``biopython`` version 1.65 or latest
 * ``pyfaidx`` version 0.3.7 or latest
+* ``drmaa`` version 0.7.6 or latest
 
 .. note::
 
@@ -43,8 +37,11 @@ management):
 Installing in a virtual environment
 ------------------------------------
 
-Using pyvenv
-^^^^^^^^^^^^^
+
+.. _install-pyvenv:
+
+Using python's pyvenv
+^^^^^^^^^^^^^^^^^^^^^^
 
 The following commands should successfully create a virtual environment and
 activate it, as long as Python 3 was previously installed on the machine.
@@ -75,7 +72,10 @@ command:
    pip install biopython
    pip install pyfaidx
    pip install matplotlib
+   pip install drmaa
+
 
+.. _install-miniconda:
 
 Using Miniconda
 ^^^^^^^^^^^^^^^^
@@ -126,6 +126,7 @@ command:
    conda install -y statsmodels
    conda install -y biopython
    conda install -y matplotlib
+   conda install -y drmaa
    pip install --no-deps pyfaidx
    pip install --no-deps lifelines
 
@@ -186,16 +187,16 @@ command (depending of the installation method). Don't forget to first activate
 the python virtual environment.
 
 
-Pyvenv
-^^^^^^^
+Using python's pyvenv
+^^^^^^^^^^^^^^^^^^^^^^
 
 .. code-block:: bash
 
    pip install -U genipe
 
 
-Miniconda
-^^^^^^^^^^
+Using Miniconda
+^^^^^^^^^^^^^^^^
 
 .. code-block:: bash
 

docs/module_content/genipe.tools.rst

@@ -36,3 +36,12 @@ genipe.tools.imputed_stats module
     :undoc-members:
     :show-inheritance:
 
+
+genipe.tools.genipe_tutorial
+-----------------------------
+
+.. automodule:: genipe.tools.genipe_tutorial
+    :members:
+    :undoc-members:
+    :show-inheritance:
+

docs/tutorials.rst

@@ -25,7 +25,7 @@ genome-wide imputation of genotypes. It describes in detail the expected input
 and output files.
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
 
    tutorials/tutorial_genipe
 
@@ -40,7 +40,7 @@ Cox's proportional hazard model). It describes in detail the expected input and
 output files.
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
 
    tutorials/tutorial_cox
 
@@ -54,7 +54,7 @@ This tutorial walks through a full example of a typical SKAT analysis while
 describing the expected input and output files.
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
 
    tutorials/tutorial_SKAT
 
@@ -69,7 +69,7 @@ This tutorial walks through a full example of a linear regression analysis
 output files.
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
 
    tutorials/tutorial_linear
 
@@ -84,7 +84,7 @@ This tutorial walks through a full example of a logistic regression analysis
 detail the expected input and output file.
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
 
    tutorials/tutorial_logistic
 
@@ -98,7 +98,7 @@ This tutorial walks through a full example of a linear mixed effects analysis.
 It describes in detail the expected input and output files.
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
 
    tutorials/tutorial_mixedlm
 
@@ -113,7 +113,7 @@ from imputation files. It describes in detail the expected input and output
 file.
 
 .. toctree::
-   :maxdepth: 3
+   :maxdepth: 2
 
    tutorials/tutorial_extract
 

docs/tutorials/tutorial_SKAT.rst

@@ -1,18 +1,10 @@
-SKAT Tutorial
-==============
 
-Quick navigation
------------------
+.. contents:: Quick navigation
+   :depth: 2
 
-1. :ref:`skat-tut-1`
-2. :ref:`skat-tut-2`
-3. :ref:`skat-tut-3`
-4. :ref:`skat-tut-4`
-5. :ref:`skat-tut-5`
-6. :ref:`skat-tut-6`
 
-SKAT analysis tutorial
------------------------
+SKAT analysis
+==============
 
 `SKAT <http://www.hsph.harvard.edu/skat/>`_ is a very popular test for the
 association of sets of rare and common variants. In :py:mod:`genipe`, we
@@ -27,10 +19,10 @@ step.
 .. _skat-tut-1:
 
 Input files generated by genipe
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+--------------------------------
 
 Impute2
-""""""""
+^^^^^^^^
 
 After running the pipeline, you should have an `Impute2` file containing
 genotype probabilities for all the imputed variants. The general structure of
@@ -73,7 +65,7 @@ be the minor allele.
     to facilitate the description of the format.
 
 Samples file
-"""""""""""""
+^^^^^^^^^^^^^
 
 This file is generated by :py:mod:`genipe` and has the ``.sample`` extension.
 It greatly resembles the PLINK ``fam`` file for those who are familiar with
@@ -122,7 +114,7 @@ assume that the A1 is the major allele, which is not true in practice):
     the major allele, which is often not true in practice.
 
 Good sites file
-""""""""""""""""
+^^^^^^^^^^^^^^^^
 
 The `.good_sites` file is also generated by :py:mod:`genipe`. It contains a
 single column representing the name of the variants that passed the quality
@@ -135,7 +127,7 @@ tool.
 .. _skat-tut-2:
 
 Creating a SNP sets file
-^^^^^^^^^^^^^^^^^^^^^^^^^
+-------------------------
 
 SKAT is based on the analysis of a "SNP set". This is simply an arbitrary set
 of variants that is created by the user. All of the variants in a same SNP set
@@ -195,7 +187,7 @@ provide them in the SNP set file as shown here.
 .. _skat-tut-3:
 
 Format for the phenotypes file
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+-------------------------------
 
 The last required file is the phenotype file. The latter contains information
 on the phenotype of interest for all the samples included in the analysis. The
@@ -227,7 +219,7 @@ the ``--outcome-type`` argument which can be set to `discrete` or `continuous`.
 .. _skat-tut-4:
 
 Running the script
-^^^^^^^^^^^^^^^^^^^
+-------------------
 
 Once all of this is ready, you can finally run the script. A sample command
 for the analysis described throughout this tutorial is the following:
@@ -290,7 +282,7 @@ The line by line explanation of this command is as follows:
 .. _skat-tut-5:
 
 Results
-^^^^^^^^
+--------
 
 After running this analysis, a file named `my_skat_analysis.skat.dosage` should
 appear. This file will contain an association p-value for every one of the
@@ -324,7 +316,7 @@ new interesting feature, please send us a push request from Github.
 .. _skat-tut-6:
 
 Usage
-^^^^^^
+------
 
 The following command will display the documentation for the SKAT analysis in
 the console:
@@ -342,7 +334,7 @@ the console:
                              {continuous,discrete} [--skat-o] --pheno-name NAME
 
    Uses the SKAT R package to analyze user defined gene sets. This script is part
-   of the 'genipe' package, version 1.2.2).
+   of the 'genipe' package, version 1.2.3).
 
    optional arguments:
      -h, --help            show this help message and exit