fredhutchio/argo-navis

Name: argo-navis

Owner: fredhutch.io

Description: A Galaxy tool for discrete trait analysis using BEAST.

Created: 2015-02-20 21:00:37.0

Updated: 2017-04-05 23:09:40.0

Pushed: 2015-10-12 22:06:18.0

Homepage: null

Size: 3768

Language: Python

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README

Argo Navis

Argo Navis is a set of Galaxy tools to carry out Bayesian discrete phylogenetic trait analyses using BEAST2 to sample posteriors and 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

 enter the newly-created directory with `cd galaxy`.

2. Next clone _this_ repo into `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:

atypes_config_file = config/datatypes_conf.xml

l_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:

types_config_file = <whateveryouhadbefor>,tools/argo-navis/datatypes_conf.xml
_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:

dir -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:

ome/galaxy/tool_deps/argo_env/0.1/venv/bin/activate
BS=/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 on the Galaxy wiki.