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| -+---------------------------------------------------------------------+ | ||
| -| ____ __ __ ___________ ______ | | ||
| -| / __ \/ /_ __ __/ /____ / ____/ ___// ____/ | | ||
| -| / /_/ / __ \/ / / / // __ \/ / \__ \/ /_ | | ||
| -| / ____/ / / / /_/ / // /_/ / /___ ___/ / __/ | | ||
| -| /_/ /_/ /_/\__, /_/ \____/\____//____/_/ | | ||
| -| /____/ | | ||
| -| | | ||
| -| http://compbio.mit.edu/PhyloCSF | | ||
| -+---------------------------------------------------------------------+ | ||
| + +---------------------------------------------------------------------+ | ||
| + | ____ __ __ ___________ ______ | | ||
| + | / __ \/ /_ __ __/ /____ / ____/ ___// ____/ | | ||
| + | / /_/ / __ \/ / / / // __ \/ / \__ \/ /_ | | ||
| + | / ____/ / / / /_/ / // /_/ / /___ ___/ / __/ | | ||
| + | /_/ /_/ /_/\__, /_/ \____/\____//____/_/ | | ||
| + | /____/ | | ||
| + | | | ||
| + | http://compbio.mit.edu/PhyloCSF | | ||
| + +---------------------------------------------------------------------+ | ||
| SOURCE DISTRIBUTION | ||
| -Please see our web site for more information about PhyloCSF. Compiling | ||
| -this software from source may be difficult for most users, because it | ||
| -requires an Objective Caml toolchain that's probably not already | ||
| -present on your system. For this reason, we provide digitally-signed | ||
| -32-bit and 64-bit Linux executables on our web site. | ||
| - | ||
| -The 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 | ||
| +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: | ||
| -[1A] Install various dependencies (Ubuntu 11.10+) | ||
| - | ||
| -Install these packages using apt-get: | ||
| -ocaml-findlib libocamlgsl-ocaml-dev libbatteries-ocaml-dev make | ||
| - | ||
| -[1B] Install various dependencies (other Linux, Mac OS X) | ||
| - | ||
| -* Objective Caml 3.11+, with native code compiler | ||
| -* OCaml findlib | ||
| -* OCaml Batteries Included 1.20+ | ||
| -- GNU Scientific Library | ||
| -- ocamlgsl 0.60 http://oandrieu.nerim.net/ocaml/gsl/ocamlgsl-0.6.0.tar.gz | ||
| - | ||
| -* These can be set up using GODI: http://godi.camlcity.org/ | ||
| - | ||
| -[2] Configure OCaml findlib | ||
| +[1] Install the OCaml package manager OPAM | ||
| -If you installed findlib (OCaml's package manager) using the Ubuntu | ||
| -packages, or another method that led to system-wide installation, you | ||
| -must set some environment variables to make it use a directory to which | ||
| -you have write access. (Alternatively, you can complete the subsequent | ||
| -steps as root, e.g. using sudo) | ||
| +http://opam.ocamlpro.com/doc/Quick_Install.html | ||
| - export OCAMLPATH=$HOME/opt/lib/ocaml # or whatever | ||
| - mkdir -p $OCAMLPATH | ||
| - export OCAMLFIND_DESTDIR=$OCAMLPATH | ||
| +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) | ||
| -To verify your configuration, run | ||
| +[2] Install dependencies using OPAM | ||
| - ocamlfind printconf | ||
| +opam install batteries gsl-ocaml twt | ||
| -"Packages will be installed in" should be a directory you can write to, | ||
| -and that same directory should appear in "Search path". | ||
| +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 | ||
| -PhyloCSF.ARCH in this directory, where e.g. ARCH = Linux.x86_64. | ||
| +PhyloCSF.ARCH in this directory, where e.g. ARCH = Linux.x86_64. This | ||
| +executable should be usable by anyone on the same machine/cluster; they don't | ||
| +have to set up OPAM or anything else. |
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