Phyloseminar notes

Giving the phyloseminar today.
Here are some instructions for the phylo seminar demos
get input files from here
http://blackrim.org/datafiles/phylo_seminar_files2014.tar.gz

get taxonomy from here
http://files.opentreeoflife.org/ott/

git clone https://github.com/OpenTreeOfLife/treemachine.git
git clone https://github.com/OpenTreeOfLife/gcmdr.git
git clone https://blackrim@bitbucket.org/blackrim/avatol_nexsons.git

cd ../treemachine
./mvn_cmdline.sh

#DEMO 1 -- atol trees
cd treemachine
java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar justtrees atol/RAxML_bootstrap.WITH_MT_BS100.rr T life atol.db
java -jar target/treemachine-0.0.1-SNAPSHOT-jar-with-dependencies.jar graphml life atol.graphml F atol.db

#DEMO 2 -- tree + taxonomy
cd ../gcmdr
edit config file (the demo one is called stephen_laptop_conf.py)
edit load_taxonomy.py and synth_one_study.py to import your conf file
python load_taxonomy.py
python synth_one_study.py

#DEMO 3 -- birds
cd ../treemachine
bash DEMO_run_birds_example.sh

#DEMO 4
web site here http://files.opentreeoflife.org/