Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

http://molpopgen.github.io/libsequence/

libsequence: a C++ class library for evolutionary genetic analysis
http://molpopgen.github.io/libsequence/

Last synced: about 2 months ago
JSON representation

libsequence: a C++ class library for evolutionary genetic analysis

Lists

README 

        
# libsequence - A C++ class library for evolutionary genetic analysis



  Copyright (C) 2002 Kevin Thornton



  libsequence2 is free software; you can redistribute it and/or modify

  it under the terms of the GNU General Public License as published by

  the Free Software Foundation; either version 3 of the License, or

  (at your option) any later version.



  This program is distributed in the hope that it will be useful,

  but WITHOUT ANY WARRANTY; without even the implied warranty of

  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

  GNU General Public License for more details.



  You should have received a copy of the GNU General Public License

  along with this program; if not, write to the Free Software

  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA



Comments are welcome.



	- Kevin Thornton 



# User's group



Please post to the [libsequence user group](https://groups.google.com/forum/#!forum/libsequence-users) for help.



# Build status



* master branch: [![Build Status](https://travis-ci.org/molpopgen/libsequence.svg?branch=master)](https://travis-ci.org/molpopgen/libsequence)

. master branch on Circle: [![CircleCI](https://circleci.com/gh/molpopgen/libsequence/tree/master.svg?style=svg)](https://circleci.com/gh/molpopgen/libsequence/tree/master)

* dev branch: [![Build Status](https://travis-ci.org/molpopgen/libsequence.svg?branch=dev)](https://travis-ci.org/molpopgen/libsequence)

. dev branch on Circle: [![CircleCI](https://circleci.com/gh/molpopgen/libsequence/tree/dev.svg?style=svg)](https://circleci.com/gh/molpopgen/libsequence/tree/dev)



# Citation



If you use the library for your research, please cite:



@article{libsequence,

author = {Thornton, Kevin},

title = {{Libsequence: a C++ class library for evolutionary genetic analysis.}},

journal = {Bioinformatics (Oxford, England)},

year = {2003},

volume = {19},

number = {17},

pages = {2325--2327},

month = nov

}



The manuscript is available online at http://bioinformatics.oxfordjournals.org/content/19/17/2325.short



## Revision history.



The revision history of the library is [here](REVISION_HISTORY.md).  The document describes what changed for a given release.



## Obtaining the source code



### Obtaining the master branch

You have a few options:



* Clone the repo (best option): git clone https://github.com/molpopgen/libsequence.git

* Click on "Download Zip" at https://github.com/molpopgen/libsequence



### Obtaining a specific release

Again, a few options:



* Click on "Releases" at https://github.com/molpopgen/libsequence, then download the one you want

* Clone the repo (see previous section)

* Get a list of releases by saying "git tag -l"

* Checkout the release you want.  For example "git checkout 1.8.0"



## Installation



### Dependencies



1. A C++11-compliant compiler (see next section)



### Compilers



I support the following compilers:



* [GCC](http://gcc.gnu.org)

* [clang](http://clang.llvm.org)



I'd appreciate success/failure reports on Intel's icc compiler. As it is no longer free for academic use, I'm not longer

able to test it.



### Simplest installation instructions



~~~

./configure

make

sudo make install

~~~



The build conditions can be adjusted via the usual environment variables.  To compile an optimized "release" build:



~~~

./configure CXXFLAGS="-O3 -DNDEBUG"

~~~



To compile a debugger-friendly build:



~~~

./configure CXXFLAGS="-O0 -g"

~~~



To change the compiler, set the C and C++ compiler variables:



~~~

./configure CC=gcc CXX=g++

~~~



#### Compiling unit tests and examples



To compile unit testing suite and example programs



~~~

make check

~~~



or



~~~

cd test

make check

~~~



Note that the library must be built prior to "make check", but _you do not have to install the library prior ot "make check"_.  The examples and unit tests are statically-linked to the version of the library that will be found in src/.libs after a "make" command.  I do this so that one can perform unit tests without having to install the library.  I use static linking here to avoid any possible confusion with an existing libsequence installation.



#### Running the unit tests



~~~

cd test && sh runTests.sh

~~~



### More complex installation scenarios



Some users may not have the dependent libraries installed in the standard locations on their systems.  Note that "standard" means wherever the compiler system looks for header files during compilation and libraries during linking.  This scenario is common on OS X systems where users have used some sort of "system" to install various libraries rather than installing from source directly.  In order to accomodate such situations, the user must provide the correct path to the include and lib directories.  For example, assume that the dependend libraries are in /opt on your system.  You would install libsequence as follows:



CPPFLAGS=-I/opt/include LDFLAGS="$LDFLAGS -l/opt/lib" ./configure



make



~~~

sudo make install

~~~



Note that the modification of LDFLAGS prepends the current value of LDFLAGS if it exists.  This allows for scenarios where the system's search path for libraries may have been modified by the user or sysadmin via a modification of that shell variable.  (One could also do the same with CPPFLAGS, FYI.)



### Installing libsequence locally



If you do not have permission to "sudo make install", you can install the library in your $HOME:



./configure --prefix=$HOME



Then, when compiling any program using libsequence, you need to add



~~~

-I$HOME/include

~~~

to any compilation commands and



~~~

-L$HOME/lib -Wl,-rpath,$HOME/lib

~~~



to any linking commands.



When running programs linking to any of the above run-time libraries, and depending on your system, you may also need to adjust variables like LD_LIBRARY_PATH to prepend $HOME/lib to them, etc., but you'll need to figure that out on case-by-case basis, as different systems can behave quite differently.



## Installation via Bioconda



Libsequence is available for installation via [bioconda](https://bioconda.github.io/):



```sh

conda install -c bioconda libsequence

```



The above command will give you the most recent stable release on OS X or Linux.



## Using libsequence to compile other programs



If libsequence is not installed in a standard path, then you must provide the appropriate include (-I) and link path (-L) commands to your compiler.  This may be done in various ways, e.g., via a configure script or your own Makefile.



A program that depends on libsequence must provide at least the following libraries to the linker:



~~~

-lsequence -lz 

~~~