phytoshell

Phytoshell Docker image configuration for setting up computing environments for CyVerse and Open Science Grid

[TODO: describe purpose of image, usage, summarize wrapper/runner, re-format with markdown language]

Summary

Docker image OS

• Ubuntu 16.04
  
  • NOTE: the Singularity container that this Docker image converts to when running on OSG currently supports up to 16.04
    

Support for 5 languages:

• Matlab Compiler Runtime (MCR) R2017b
  
• Python 2.7/3.6.5 (from Anaconda3-5.2.0 [conda 4.5.11])
  
• R 3.2.2
  
• Octave 4.2.2
  
• Julia 1.0.0
  

iRODS Commands

• 4.1.9 (supports Ubuntu 14+)
  
  • NOTE: version 4.1.10 and 4.1.11 have bugs when mounting with FUSE
  • Future versions will be updated to 4.2.X
    

Installation

A) Download un-compiled docker image from GitHub

1. Clone this repository into desired folder
   git clone https://github.com/jbustamante35/phytoshell
2. Build docker image
   docker build -t [name-for-image] /path/to/Dockerfile
3. Run docker image
   docker run -it [name-for-image] [verobisty] [codebase] [application-instructions (see Usage)]

B) Pull pre-compiled docker image from DockerHub

1. Pull repository from DockerHub
   docker pull jbustamante35/testphytoshell
2. Run docker image
   docker run -it [name-for-image] [verobisty] [codebase] [application-instructions (see Usage)]

Running applications with interactive GUI

To run this container with applications that require an interactive GUI, change the run command to:

docker run --privileged -p 22:22 -it [name-of-image] [verobisty] [codebase] [application_config (see Usage)]

Then in a separate terminal, ssh into the running container with X11 port forwarding

ssh -CX root@localhost

---

Alternatively, create a profile in ~/.ssh/config with the following settings

Host dok
     HostName localhost
     Port 22
     User root
     ForwardX11 yes
     SendEnv LANG LC_*
     HashKnownHosts yes
     GSSAPIAuthentication yes

---

Then ssh into the running container

ssh -C dok

Run Arguments

Running the container requires the following arguments [ explained in detail in runner script ] name-of-image: name of docker image
- if running a manually-built docker container, this is your docker image name.
- if running the pre-compiled docker image, the default image is phytoshell.

verbosity: iRODS download verbosity level
for downloading from iRODS [ 0 for none ; 1 for verbose ]

codebase:
iRODS

application_config:
asdf

Authors

Nathan Miller, Senior Scientist (ndmill@gmail.com)
University of Wisconsin - Madison
Department of Botany

Julian Bustamante, Cellular and Molecular Biology Program (jbustamante@wisc.edu)
University of Wisconsin - Madison
Department of Botany

License

MIT license found in LICENSE