fastlmm 0.1.6

Fast GWAS

fastlmm overview

This package includes FaST-LMM-SELECT and FaST-LMM-SET.

If you want to test single SNPs, please use the C++ version for now.

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Package Install Instructions:
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fastlmm has the following dependencies:

python 2.7

Packages:

numpy
scipy
matplotlib
pandas
scikit.learn (sklearn)
cython
[statsmodels -- install only required for logistic-based tests, not the standard linear LRT]

Please see MANUAL.txt for usage instructions.

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(1) Installation of dependent packages
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We highly recommend using a python distribution such as
Anaconda (https://store.continuum.io/cshop/anaconda/)
or Enthought (https://www.enthought.com/products/epd/free/).
Both these distributions can be used on linux and Windows, are free
for non-commercial use, and optionally include an MKL-compiled distribution
for optimal speed. This is the easiest way to get all the required package
dependencies.

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(2) Building source extension code (i.e. non-python code that gets called from python)
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Go to the directory where you copied the source code for fastlmm.

On linux:

At the shell, type: "sudo python setup.py install"

On Windows:

At the OS command prompt, type "python setup.py install"


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For developers (and also to run regression tests)
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When working on the developer version, first add the src directory of the package to your PYTHONPATH
environment variable.

For building C-extensions, first make sure all of the above dependencies are installed (including cython)

To build extension (from .\src dir), type the following at the OS prompt:
"python setup.py build_ext --inplace"

Note, if this fails with a gcc permission denied error, then specifying the correct compiler will
likely fix the problem. For e.g. "python setup.py build_ext --inplace --compiler=msvc"

Don't forget to set your PYTHONPATH to point to the directory above the one named fastlmm in
the fastlmm source code. For e.g. if fastlmm is in the [somedir] directory, then
in the unix shell use "export PYTHONPATH=$PYTHONPATH:[somedir]". Or in the Windows DOS terminal,
one can use DOS: "set PYTHONPATH=%PYTHONPATH%;[somedir]" (or use the Windows GUI for env variables).

**Note for Windows: You must have Visual Studio installed. If you have VisualStudio2008 installed
(which was used to build python2.7) you need to nothing more. Otherwise, follow these instructions:

If you have Visual Studio 2010 installed, execute:
SET VS90COMNTOOLS=%VS100COMNTOOLS%

or with Visual Studio 2012 installed:
SET VS90COMNTOOLS=%VS110COMNTOOLS%

or with Visual Studio 2013 installed:
SET VS90COMNTOOLS=%VS120COMNTOOLS%


Running regression tests
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From the directory tests at the top level, run "python test.py". This will run a
series of regression tests, reporting "." for each one that passes, "F" for each
one that does not match up, and "E" for any which produce a run-time error. After
they have all run, you should see the string "............" indicating that they
all passed, or if they did not, something such as "....F...E......", after which
you can see the specific errors.

Note that you must use "python setup.py build_ext --inplace" to run the
regression tests, and not "python setup.py install".