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Dependencies
------------

On debian type systems (including Ubuntu), add the following packages if they are not already installed (or have your admin add them if you do not have permission):

sudo apt-get install g++ libssl-dev libcurses-perl zlib1g-dev

Building
--------

To compile, from the top level directory, type: make
To test (after compiling), from the top level directory, type: make test

Under the main statgen repository, there are: 
* lib - the library code
** The library code is compiled into libStatGen.a which, after compiling is located at: statgen/lib/libStatGen.a
** After compiling, library headers can all be found in: statgen/lib/include
* src - the tools we developed
** After compling, the executables are found in: statgen/src/bin
* scripts - the scripts we developed

Makefiles
---------
statgen/Makefile.include should contain the definitions that you need for creating software using this library.

statgen/lib/Makefile.lib and statgen/lib/Makefile.src can be used as templates for creating Makefiles for new software.  If possible, just link to them.  They look for a file called Makefile.tool that should be all you need to update for your specific software.  (both Makefiles automatically include Makefile.include)

A similar setup should be used for test code, linking your Makefile to statgen/Makefile.test and defining Makefile.testtool for your specific test.

Other Notes
-----------
* Typically the .o files are compiled into their own directory called obj.

Center for Statistical Genetics's Projects

fivex icon fivex

Interactive eQTL visualizations

gotcloud icon gotcloud

Genomes on the Cloud, Mapping & Variant Calling Pipelines

gvs-public icon gvs-public

The public base of gvs, which does not contain any secret keys or emails

htslib icon htslib

C library for high-throughput sequencing data formats

imputationserver icon imputationserver

TOPMED Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity

laser icon laser

Locating Ancestry from SEquence Reads

ldserver icon ldserver

Fast API server for calculating linkage disequilibrium

libstatgen icon libstatgen

Useful set of classes for creating statistical genetic programs.

localzoom icon localzoom

Make interactive LocusZoom plots from a local GWAS file

locuszoom icon locuszoom

A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.

metal icon metal

Meta-analysis of genomewide association scans

minimac3 icon minimac3

Minimac3 is a low memory and computationally efficient implementation of the genotype imputation algorithms. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.

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