/PhyloCSF

Permalink
PhyloCSF/README
Newer
Older
Raw Normal view History
100644 57 lines (42 sloc) 2.54 KB
Mar 19, 2013 @mlin README with simplified build instructions
1 +---------------------------------------------------------------------+
2 | ____ __ __ ___________ ______ |
3 | / __ \/ /_ __ __/ /____ / ____/ ___// ____/ |
4 | / /_/ / __ \/ / / / // __ \/ / \__ \/ /_ |
5 | / ____/ / / / /_/ / // /_/ / /___ ___/ / __/ |
6 | /_/ /_/ /_/\__, /_/ \____/\____//____/_/ |
7 | /____/ |
8 | |
9 | http://compbio.mit.edu/PhyloCSF |
10 +---------------------------------------------------------------------+
Aug 13, 2010 initial import
11
12 SOURCE DISTRIBUTION
13
Mar 19, 2013 @mlin README with simplified build instructions
14 Please see our web site for more information about PhyloCSF and how to use it.
15 PhyloCSF is written in OCaml. This source distribution is divided into a
16 library, CamlPaml, containing generic infrastructure for phylogenetic rate
17 models, and a program implementing the PhyloCSF-specific models and driver
18 program. With additional development, the CamlPaml library will eventually be
Mar 21, 2012 @mlin fix ocaml+twt submodule and update README with more detailed instruct…
19 released as a separate entity, but for now it is just part of this
20 distribution.
21
22 Here are the steps to build the source:
23
Mar 19, 2013 @mlin README with simplified build instructions
24 [1] Install the OCaml package manager OPAM
Mar 21, 2012 @mlin fix ocaml+twt submodule and update README with more detailed instruct…
25
Mar 19, 2013 @mlin README with simplified build instructions
26 http://opam.ocamlpro.com/doc/Quick_Install.html
Mar 21, 2012 @mlin fix ocaml+twt submodule and update README with more detailed instruct…
27
Mar 19, 2013 @mlin README with simplified build instructions
28 This will install a minimal OCaml toolchain (if not already present on your
29 system) and the OPAM package manager. Once it's installed, initialize your
30 shell environment by running: eval $(opam config env)
Mar 21, 2012 @mlin fix ocaml+twt submodule and update README with more detailed instruct…
31
Mar 19, 2013 @mlin README with simplified build instructions
32 [2] Install dependencies using OPAM
Mar 21, 2012 @mlin fix ocaml+twt submodule and update README with more detailed instruct…
33
Apr 24, 2013 @mlin Update README
34 opam install batteries ocaml+twt gsl
Mar 21, 2012 @mlin fix ocaml+twt submodule and update README with more detailed instruct…
35
Apr 24, 2013 @mlin Update README
36 The gsl package may require you to separately install the GNU Scientific
Mar 19, 2013 @mlin README with simplified build instructions
37 Library (GSL) from: http://www.gnu.org/software/gsl/
38 On Debian/Ubuntu systems GSL is available in the 'libgsl0-dev' package, and on
39 Mac OS X, 'gsl' is available in both Homebrew and MacPorts.
Mar 21, 2012 @mlin fix ocaml+twt submodule and update README with more detailed instruct…
40
Aug 24, 2012 @mlin Makefile: build ocaml+twt automatically
41 [3] Compile PhyloCSF
Aug 13, 2010 initial import
42
Mar 21, 2012 @mlin fix ocaml+twt submodule and update README with more detailed instruct…
43 Now just run 'make' in this directory. This will build and install the
44 CamlPaml library, then compile the PhyloCSF executable and copy it to
Mar 19, 2013 @mlin Add dispatch script to set PHYLOCSF_BASE
45 this directory. You can then use the ./PhyloCSF dispatch script like the
46 examples found on our website, e.g.
47
48 ./PhyloCSF 12flies PhyloCSF_Examples/tal-AA.fa
49
50 PhyloCSF should be usable in this way by anyone on the machine/cluster with rx
51 permissions; they don't have to set up OPAM or anything else. PhyloCSF can
52 be started from any working directory.
53
54 If you want to 'install' PhyloCSF somewhere, you must transplant PhyloCSF,
55 PhyloCSF.ARCH (where e.g. ARCH=Linux.x86_64), and the PhyloCSF_Parameters
56 directory to the desired location.