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+# Argo Navis
+
+**Argo Navis** is a set of Galaxy tools to carry out Bayesian discrete phylogenetic trait analyses using [BEAST2](http://beast2.org) to sample posteriors and [PACT](http://bedford.io/projects/PACT/) to extract information from these posteriors.
+For background and more information, please see the help section of the `introduction.xml` "tool".
+
+## Dependencies
+
+Before running Argo Navis in either dev or production, there are a number of dependencies which must be installed:
+
+* BEAST2, and the BEAST_CLASSIC package
+* PACT
+* R, and the following libraries
+    * RColorBrewer
+    * ggplot2
+    * gtable
+    * argparse
+* python, and the following libraries
+    * alnclst
+    * biopython
+    * biopy
+    * numpy
+    * csvkit
+    * svg_stack.py
+* inkscape
+* java
+
+Java, Inkscape, and R must all be installed.
+For all the other dependencies, the `env/envbootstrap.sh` can be run to set up a virtualenv which contains the rest of the dependencies.
+
+
+## Running in dev mode
+
+### 1. Clone the Galaxy repository
+
+```git clone https://github.com/galaxyproject/galaxy.git```
+
+Then enter the newly-created directory with `cd galaxy`.
+
+### 2. Next clone _this_ repo into `tools/argo-navis`
+
+```git clone https://github.com/fredhutchio/argo-navis.git tools/argo-navis```
+
+Galaxy is a bit picky about where things live, so make sure you get the path right.
+
+### 3. Setup your `galaxy.ini` file
+
+Copy over `config/galaxy.ini.sample` to `config/galaxy.ini`
+In your copy now, look for the following lines:
+
+```
+#datatypes_config_file = config/datatypes_conf.xml
+...
+#tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml
+```
+
+First, uncomment these and add `.sample` to the end of each of these files.
+Then, add the `datatypes_conf.xml` and `tool_conf.xml` files to the end of these lines so they look like this:
+
+```
+datatypes_config_file = <whateveryouhadbefor>,tools/argo-navis/datatypes_conf.xml
+tool_config_file = <whateveryouhadbefor>tools/argo-navis/tool_conf.xml
+```
+
+#### b) Friendly hosts/ports
+
+By default, the server will run on `127.0.0.1`.
+To easily access this server over the network, you can change this to `0.0.0.0` by uncommenting `#host=...` line on the 36 line of the `ini` file (there are other `host` settings, so make sure you get the right one) and setting it to `0.0.0.0`.
+If you're running in a local network on a computer named `servername`, you will now be able to access the server on `servername:8080`.
+You can also edit the `port` variable around line 31 if you need a port other than 8080, the default.
+
+#### c) Consider activating the watch tools
+
+Just uncomment the line `#watch_tools = False` and set to `True`.
+You will need to install `watchdog` for this to work, if not already installed on your system.
+It's a python library; Look it up.
+
+### 4. Run it!
+
+`sh run.sh` and observe the awesomeness!
+
+
+## Setting up on an existing Galaxy deployment
+
+If you already have an existing Galaxy deployment, you should be able to just clone the repo, and modify the datatypes and tool config lines in your `ini` file, as explained above.
+
+If you've configured your Galaxy instance for installation of tools from the Galaxy toolsheds, you can use the `env/envbootstrap.sh` script mentioned above to install Argo Navis's dependencies (except Java, Inkscape, and R) to Galaxy's `tool_dependency_dir`.
+
+Say your `tool_dependency_dir` is in `/home/galaxy/tool_deps`.
+Create a directory called `argo_env/0.1` in this directory:
+
+```
+$ mkdir -p /home/galaxy/tool_deps/argo_env/0.1
+```
+
+Use the bootstrap script to create the virtualenv in the new directory:
+
+```
+$ ./env/envbootstrap.sh --venv /home/galaxy/tool_deps/argo_env/0.1/venv
+```
+
+This will take a while.
+Once the bootstrap script finishes, create an `env.sh` file in `/home/galaxy/tool_deps/argo_env/0.1` with the following contents:
+
+```
+. /home/galaxy/tool_deps/argo_env/0.1/venv/bin/activate
+R_LIBS=/home/galaxy/tool_deps/argo_env/0.1/venv/lib/R ; export R_LIBS
+```
+
+Galaxy will automatically source this file just before executing the tool command line in order to set up the job environment.
+For more information on how this works, see the [tool dependencies page](https://wiki.galaxyproject.org/Admin/Config/ToolDependencies) on the Galaxy wiki.