Difference between revisions of "TreemixTutorial"
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= TREEMIX = | = TREEMIX = | ||
− | download | + | Program download: [ https://bitbucket.org/nygcresearch/treemix/wiki/Home goto the TREEMIX website]<br |
+ | Tutorial material: download [http://peterbeerli.com/classdata/ISC5935ppg/dadi_tutorial.zip DADI_TUTORIAL.ZIP]'''<br> | ||
+ | |||
+ | download the software as a tar.gz file is here: https://bitbucket.org/nygcresearch/treemix/downloads/treemix-1.12.tar.gz a git repository can be cloned like this: git clone https://bitbucket.org/nygcresearch/treemix.git | ||
* unpack and/or cd into the folder: the treemix program needs additional libraries that are most likely not on your computer if you don't develop code. but try anyway first this: | * unpack and/or cd into the folder: the treemix program needs additional libraries that are most likely not on your computer if you don't develop code. but try anyway first this: |
Revision as of 06:54, 23 September 2015
TREEMIX
Program download: [ https://bitbucket.org/nygcresearch/treemix/wiki/Home goto the TREEMIX website]<br
Tutorial material: download DADI_TUTORIAL.ZIP
download the software as a tar.gz file is here: https://bitbucket.org/nygcresearch/treemix/downloads/treemix-1.12.tar.gz a git repository can be cloned like this: git clone https://bitbucket.org/nygcresearch/treemix.git
- unpack and/or cd into the folder: the treemix program needs additional libraries that are most likely not on your computer if you don't develop code. but try anyway first this:
./configure
if this breaks, check out what is missing: you may need to install the gnu scientific library: for example like this (the website is http://www.gnu.org/software/gsl/)
wget http://gnu.mirror.iweb.com/gsl/gsl-1.16.tar.gz then tar -xvfz gsl-1.16.tar.gz cd into gsl-1.16 read the README and INSTALL ./configure make make install # you may need sudo
if BOOST breaks then try this - figure out whether you have boost on your system, usually in /usr/local/boost - if not then install boost from here http://www.boost.org/build/ download a recent version for your system read: http://www.boost.org/doc/libs/1_55_0/doc/html/bbv2/installation.html
now try again you may need to do things like this
./configure --with-boost=/usr/local/boost --with-boostlib=/usr/local/boost/lib
Once all is installed, then read the manual in the treemix folder, the manual gives a short overview of the dataformat. See also our tutorial file example1.treemix.gz
commands to try are:
treemix -i example1.treemix -k 500 treemix -i example1.treemix -k 500 -o mytest -m 4
Once treemix has run, fire up R (I used R.app on my mac)
use (you will need to set the working path:
source("~/src/treemix/src/plotting_funcs.R")
plot_tree("mytest")
Explore what we can do with the output!