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INSTALL
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profillic relies on a number of other libraries. All are open source
and are easy to install.
Required external libraries:
---
BOOST (tested with version 1.59.0)
Seqan (direct from github)
HMMoC-BFloat-Algebra:
https://github.com/pedlefsen/HMMoC-BFloat-Algebra
Required galosh libraries:
---
prolific (NOT the same thing as this library, which is "profillic"): https://github.com/galosh/prolific
Recommended galosh libraries:
---
profuse: https://github.com/galosh/profuse
### What follows mostly assumes you're on a mac using macports. If on another system, use the analogous package manager or follow installation instructions for the required packages if you want to build them yourself.
# # PREREQ: Get BOOST!
# # On my system, the boost libraries are in /usr/local/lib, and boost
# # includes are in /usr/local/include. If your version is not
# # up-to-date, I can't vouch for this working, so you might need to
# # reinstall BOOST even if you already have it. I've tested the code
# # with version 1.59.0 (only).
#
# # If you need to uninstall an existing installation, do
# rm -r /usr/local/lib/libboost*
# rm -r /usr/local/include/boost/
sudo port install boost
## Profillic uses boost-build (bjam)
sudo port install boost-build
rehash
## Seqan needs cmake (on a mac, get it using macports [http://www.macports.org/install.php]:)
sudo port install cmake
## Using Seqan directly from github (master branch, not devel branch) [https://github.com/seqan/seqan]:
cd ~/src/from-git
git clone https://github.com/seqan/seqan.git
## Docs at http://docs.seqan.de/seqan/master/
## (unsure if you really need to make sure you have the java jde installed and up to date first: http://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html)
## (make sure boost is installed and findable before running cmake)
mkdir seqan-build
cd seqan-build/
mkdir debug
cd debug
cmake ~/src/from-git/seqan -DCMAKE_BUILD_TYPE=Debug
make seqan_tcoffee
cd ..
mkdir release
cd release
cmake ~/src/from-git/seqan -DCMAKE_BUILD_TYPE=Release
make seqan_tcoffee
cd ..
git clone https://github.com/pedlefsen/HMMoC-BFloat-Algebra.git
cd HMMoC-BFloat-Algebra
ln -s /opt/local/lib boost-lib
ln -s /opt/local/include boost-include
bjam dist release --toolset=darwin
cd ..
git clone https://github.com/galosh/prolific.git
## prolific is a header only library; there is nothing to build.
git clone https://github.com/galosh/profillic.git
=========
FINALLY, installing profillic.
cd profillic
ln -s /opt/local/lib boost-lib
ln -s /opt/local/include boost-include
ln -s ~/src/from-git/seqan seqan-trunk
ln -s ../HMMoC-BFloat-Algebra
ln -s ../prolific
## NOTE: I had to add --toolset=darwin because it wasn't guessing it correctly. You can add eg "use darwin ;" to your site-config.jam [or user-config.jam] file.
# First must make sure you can compile it in the fast-to-compile, slow-to-run "debug" variant, before trying to compile the slow-to-compile "release" variant.
bjam --clean --toolset=darwin
bjam debug profillic_AA_CQA --toolset=darwin
# If that works (fingers crossed!), do
bjam dist release --toolset=darwin
cd ..
# The above will (slowly) compile the executables, and will copy them to the dist/ subdir.
# You might be interested to check out the bjam (Boost.Build) documentation: http://www.boost.org/boost-build2/doc/html/index.html