Running the workshop docker locally

Note, these instructions are for Mac and Linux users. Windows users will need to adjust accordingly.

Download and install Docker:

You can get the docker software free here:

https://www.docker.com/community-edition

Downloading/Installing the Workshop Docker image:

Open up a terminal and run the following command:

%  docker pull trinityctat/berlin2018 

Setting up a workspace on your computer:

Create a directory in your home area:

%  cd $HOME

%  mkdir trinity_workshop

%  cd trinity_workshop

Download the sample data provided for the workshop:

%  wget https://data.broadinstitute.org/Trinity/RNASEQ_WORKSHOP/TRINITY_Berlin_2017_ws_data_bundle.tar.gz

Note, if you don't have wget installed, you can just download it directly from your web browser. If it puts it in your $HOME/Downloads/ folder, just move it here after it finishes downloading.

Unpack it:

%  tar xvf TRINITY_Berlin_2017_ws_data_bundle.tar.gz

Running the workshop docker:

Run the following command to launch a docker container:

%  docker run --rm -v `pwd`:/home/training \
      -v `pwd`/workshop_shared/shared:/home/training/shared_ro:ro \
      -v `pwd`:/var/www/html \
      -v `pwd`/workshop_shared/js:/var/www/html/js:ro \
      -v `pwd`/workshop_shared/css:/var/www/html/css:ro \
      -p 10000:22 -p 8000:80 -p 9000:443  --name trinity_user \
      trinityctat/berlin2018

When you run the above, you'll see these messages:

2018-06-15 11:50:55,055 CRIT Supervisor running as root (no user in config file)
2018-06-15 11:50:55,058 INFO supervisord started with pid 1
2018-06-15 11:50:56,064 INFO spawned: 'gateone' with pid 9
2018-06-15 11:50:56,066 INFO spawned: 'ssh' with pid 10
2018-06-15 11:50:56,068 INFO spawned: 'apache2' with pid 11
2018-06-15 11:50:56,164 INFO exited: ssh (exit status 0; not expected)
2018-06-15 11:50:56,209 INFO exited: apache2 (exit status 0; not expected)
2018-06-15 11:50:57,498 INFO success: gateone entered RUNNING state, process has stayed up for > than 1 seconds (startsecs)
2018-06-15 11:50:57,499 INFO spawned: 'ssh' with pid 116
2018-06-15 11:50:57,502 INFO spawned: 'apache2' with pid 117
2018-06-15 11:50:57,511 INFO exited: apache2 (exit status 0; not expected)
2018-06-15 11:50:57,518 INFO exited: ssh (exit status 0; not expected)
2018-06-15 11:50:59,524 INFO spawned: 'ssh' with pid 139
2018-06-15 11:50:59,526 INFO spawned: 'apache2' with pid 140
2018-06-15 11:50:59,536 INFO exited: apache2 (exit status 0; not expected)
2018-06-15 11:50:59,544 INFO exited: ssh (exit status 0; not expected)
2018-06-15 11:51:02,553 INFO spawned: 'ssh' with pid 162
2018-06-15 11:51:02,555 INFO spawned: 'apache2' with pid 163
2018-06-15 11:51:02,567 INFO exited: apache2 (exit status 0; not expected)
2018-06-15 11:51:02,571 INFO gave up: apache2 entered FATAL state, too many start retries too quickly
2018-06-15 11:51:02,572 INFO exited: ssh (exit status 0; not expected)
2018-06-15 11:51:03,574 INFO gave up: ssh entered FATAL state, too many start retries too quickly

Do not worry! this is normal. Everything is fine. :-)

You can now visit the following URLs to access the workshop linux instance running locally:

# URL for the file viewer:
http://localhost:8000/    

# URL for the ssh / terminal view:
http://localhost:9000/

The user/password for logging in is training/training

If you want to directly ssh into your instance, instead of using the terminal/ssh view, you could:

%  ssh training@localhost -P 10000

And now you should be able to do everything we did at the workshop from your own computer instead of using the cloud.

Exiting the Docker

Simply cntrl-c within the terminal that's running the docker instance. This will shut it down.