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https://github.com/shiltemann/phinch-galaxy-ie


https://github.com/shiltemann/phinch-galaxy-ie

docker interactive-environments phinch usegalaxy

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README 

        
NOTE: GIE folder is now deprecated as this has been merged into Galaxy. The Docker image is still being maintained here.



# Phinch Galaxy IE



Galaxy Interactive Environment for the [Phinch](http://phinch.org) visualisation framework.



## How to Run



### Metagenomics Galaxy



This plugin is installed in the [Metagenomics Galaxy Flavour](https://github.com/bgruening/galaxy-metagenomics). 



Assuming docker is installed on your system, this container can be started as follows:



```

docker run --rm -p 8080:80 -it -p 8800:8800 -v `pwd`/foo/:/export/ --privileged=true quay.io/bgruening/galaxy-metagenomics

```



NOTE: See the README in the Metagenomics Galaxy repo for more information and advanced configurations.



Once the image is running, access it by navigating to `:8080` in your (Chrome) web browser. Make sure you are logged in and upload a biom file. You should now have Phinch as a visualisation option for that dataset.



### How to run this on a local Galaxy



Below is a description of how to test this on a localhost Galaxy instance. For more advanced configurations, please

see the excellent documentation by the Galaxy Team [here](https://docs.galaxyproject.org/en/master/admin/interactive_environments.html).



#### Install Galaxy



```bash

$ git clone https://github.com/galaxyproject/galaxy/

```



edit the galaxi.ini file:



```

[..]



# The address on which to listen.  By default, only listen to localhost (Galaxy

# will not be accessible over the network).  Use '0.0.0.0' to listen on all

# available network interfaces.

host = 0.0.0.0



[..]



# Interactive environment plugins root directory: where to look for interactive

# environment plugins.  By default none will be loaded.  Set to

# config/plugins/interactive_environments to load Galaxy's stock plugins

# (currently just IPython).  These will require Docker to be configured and

# have security considerations, so proceed with caution. The path is relative to the 

# Galaxy root dir.  To use an absolute path begin the path with '/'.  This is a comma

# separated list.

interactive_environment_plugins_directory = config/plugins/interactive_environments



[..]



# Have Galaxy manage dynamic proxy component for routing requests to other

# services based on Galaxy's session cookie.  It will attempt to do this by

# default though you do need to install node+npm and do an npm install from

# `lib/galaxy/web/proxy/js`.  It is generally more robust to configure this

# externally managing it however Galaxy is managed.  If True Galaxy will only

# launch the proxy if it is actually going to be used (e.g. for IPython).

dynamic_proxy_manage=True



# Dynamic proxy can use an SQLite database or a JSON file for IPC, set that

# here.

dynamic_proxy_session_map=database/session_map.sqlite



# Set the port and IP for the the dynamic proxy to bind to, this must match

# the external configuration if dynamic_proxy_manage is False.

dynamic_proxy_bind_port=8800

dynamic_proxy_bind_ip=0.0.0.0



# Enable verbose debugging of Galaxy-managed dynamic proxy.

dynamic_proxy_debug=True



[..]



```



#### Set up the proxy 



```bash

$ cd /lib/galaxy/web/proxy/js

$ npm install

```



(to install node on ubuntu:)



```

$ sudo apt-get install npm



# if you get an error /usr/bin/env: not found:

$ sudo ln -s /usr/bin/nodejs /usr/bin/node

```



#### Run



Start Galaxy:



```bash

$ cd 

$ sh run.sh

```



- Open your Chrome web browser  

- Navigate to :8080  

- Make sure you are logged in  

- Upload a .biom file (an example file is provided in this repo)  

- Click on the visualisation button for the biom dataset and select Phinch  

- The first time it will download the docker image from DockerHub, which may take a little while. (you can monitor progress in Galaxy log)  

- After that it should be pretty quick to load.  

- Your galaxy dataset should be automatically loaded into Phinch  

- NOTE: share button has been disabled as the docker image will be short-lived  

- NOTE: the docker image will be killed after 10 minutes of inactivity  

- NOTE: export of filtered biom file or images should result in a new dataset in your history, but a refresh of the history may be required.