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| | ____ __ __ ___________ ______ | | |
| | / __ \/ /_ __ __/ /____ / ____/ ___// ____/ | | |
| | / /_/ / __ \/ / / / // __ \/ / \__ \/ /_ | | |
| | / ____/ / / / /_/ / // /_/ / /___ ___/ / __/ | | |
| | /_/ /_/ /_/\__, /_/ \____/\____//____/_/ | | |
| | /____/ | | |
| | | | |
| | http://compbio.mit.edu/PhyloCSF | | |
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| SOURCE DISTRIBUTION | |
| Please see our web site for more information about PhyloCSF and how to use it. | |
| PhyloCSF is written in OCaml. This source distribution is divided into a | |
| library, CamlPaml, containing generic infrastructure for phylogenetic rate | |
| models, and a program implementing the PhyloCSF-specific models and driver | |
| program. With additional development, the CamlPaml library will eventually be | |
| released as a separate entity, but for now it is just part of this | |
| distribution. | |
| Here are the steps to build the source: | |
| [1] Install the OCaml package manager OPAM | |
| http://opam.ocamlpro.com/doc/Quick_Install.html | |
| This will install a minimal OCaml toolchain (if not already present on your | |
| system) and the OPAM package manager. Once it's installed, initialize your | |
| shell environment by running: eval $(opam config env) | |
| [2] Install dependencies using OPAM | |
| opam install batteries ocaml+twt gsl-ocaml | |
| The gsl-ocaml package may require you to separately install the GNU Scientific | |
| Library (GSL) from: http://www.gnu.org/software/gsl/ | |
| On Debian/Ubuntu systems GSL is available in the 'libgsl0-dev' package, and on | |
| Mac OS X, 'gsl' is available in both Homebrew and MacPorts. | |
| [3] Compile PhyloCSF | |
| Now just run 'make' in this directory. This will build and install the | |
| CamlPaml library, then compile the PhyloCSF executable and copy it to | |
| this directory. You can then use the ./PhyloCSF dispatch script like the | |
| examples found on our website, e.g. | |
| ./PhyloCSF 12flies PhyloCSF_Examples/tal-AA.fa | |
| PhyloCSF should be usable in this way by anyone on the machine/cluster with rx | |
| permissions; they don't have to set up OPAM or anything else. PhyloCSF can | |
| be started from any working directory. | |
| If you want to 'install' PhyloCSF somewhere, you must transplant PhyloCSF, | |
| PhyloCSF.ARCH (where e.g. ARCH=Linux.x86_64), and the PhyloCSF_Parameters | |
| directory to the desired location. |