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author bcclaywell
date Mon, 12 Oct 2015 17:57:38 -0400
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1
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2 # Argo Navis
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3
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4 **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.
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5 For background and more information, please see the help section of the `introduction.xml` "tool".
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6
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7 ## Dependencies
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8
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9 Before running Argo Navis in either dev or production, there are a number of dependencies which must be installed:
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10
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11 * BEAST2, and the BEAST_CLASSIC package
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12 * PACT
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13 * R, and the following libraries
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14 * RColorBrewer
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15 * ggplot2
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16 * gtable
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17 * argparse
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18 * python, and the following libraries
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19 * alnclst
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20 * biopython
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21 * biopy
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22 * numpy
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23 * csvkit
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24 * svg_stack.py
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25 * inkscape
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26 * java
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27
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28 Java, Inkscape, and R must all be installed.
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29 For all the other dependencies, the `env/envbootstrap.sh` can be run to set up a virtualenv which contains the rest of the dependencies.
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31
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32 ## Running in dev mode
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33
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34 ### 1. Clone the Galaxy repository
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35
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36 ```git clone https://github.com/galaxyproject/galaxy.git```
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37
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38 Then enter the newly-created directory with `cd galaxy`.
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39
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40 ### 2. Next clone _this_ repo into `tools/argo-navis`
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42 ```git clone https://github.com/fredhutchio/argo-navis.git tools/argo-navis```
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44 Galaxy is a bit picky about where things live, so make sure you get the path right.
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45
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46 ### 3. Setup your `galaxy.ini` file
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47
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48 Copy over `config/galaxy.ini.sample` to `config/galaxy.ini`
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49 In your copy now, look for the following lines:
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50
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51 ```
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52 #datatypes_config_file = config/datatypes_conf.xml
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53 ...
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54 #tool_config_file = config/tool_conf.xml,config/shed_tool_conf.xml
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55 ```
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56
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57 First, uncomment these and add `.sample` to the end of each of these files.
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58 Then, add the `datatypes_conf.xml` and `tool_conf.xml` files to the end of these lines so they look like this:
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59
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60 ```
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61 datatypes_config_file = <whateveryouhadbefor>,tools/argo-navis/datatypes_conf.xml
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62 tool_config_file = <whateveryouhadbefor>tools/argo-navis/tool_conf.xml
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63 ```
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64
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65 #### b) Friendly hosts/ports
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66
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67 By default, the server will run on `127.0.0.1`.
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68 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`.
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69 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`.
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70 You can also edit the `port` variable around line 31 if you need a port other than 8080, the default.
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71
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72 #### c) Consider activating the watch tools
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73
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74 Just uncomment the line `#watch_tools = False` and set to `True`.
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75 You will need to install `watchdog` for this to work, if not already installed on your system.
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76 It's a python library; Look it up.
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77
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78 ### 4. Run it!
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79
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80 `sh run.sh` and observe the awesomeness!
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81
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82
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83 ## Setting up on an existing Galaxy deployment
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84
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85 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.
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86
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87 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`.
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88
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89 Say your `tool_dependency_dir` is in `/home/galaxy/tool_deps`.
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90 Create a directory called `argo_env/0.1` in this directory:
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91
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92 ```
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93 $ mkdir -p /home/galaxy/tool_deps/argo_env/0.1
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94 ```
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95
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96 Use the bootstrap script to create the virtualenv in the new directory:
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97
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98 ```
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99 $ ./env/envbootstrap.sh --venv /home/galaxy/tool_deps/argo_env/0.1/venv
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100 ```
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101
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102 This will take a while.
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103 Once the bootstrap script finishes, create an `env.sh` file in `/home/galaxy/tool_deps/argo_env/0.1` with the following contents:
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104
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105 ```
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106 . /home/galaxy/tool_deps/argo_env/0.1/venv/bin/activate
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107 R_LIBS=/home/galaxy/tool_deps/argo_env/0.1/venv/lib/R ; export R_LIBS
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108 ```
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109
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110 Galaxy will automatically source this file just before executing the tool command line in order to set up the job environment.
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111 For more information on how this works, see the [tool dependencies page](https://wiki.galaxyproject.org/Admin/Config/ToolDependencies) on the Galaxy wiki.