OBF Travel Fellowship – Coding in the Winter Wonderland: Galaxy Admin Training in Oslo, 2018

This blog post is syndicated from a post on Arun Decano’s blog, originally published Feb 1, 2018. Arun was supported by the ongoing OBF travel fellowship program to attend a Galaxy Admin Workshop held in Oslo, Norway Jan 7-14, 2018.

The OBF’s Travel Fellowship program continues to help open source bioinformatics software developers with funding to attend conferences, workshops, or training events. The next call closes 15 April 2018.

Sharing highlights of my unforgettable experience in the snowy white city of Oslo, Norway from the 7th to the 14th of January, 2018.

I submitted a last-minute application for the Galaxy Admin workshop in the University of Oslo so I was extremely delighted when Dr. Nygard dropped me a message confirming my place for the training. I was thrilled with both the thought of learning how to customize my own Galaxy server and traveling to the winter capital of the world!

I had a limited understanding about how Galaxy servers work as we have have our own server in the lab. But I knew that Galaxy offers various efficient pipelines for large genomic data analysis so I was  curious how to get started with it.

The facilitators of the training were very prompt in setting our expectations for the event. They constantly sent e-mails with tips on how to get around Oslo and which hotel offers the best yet affordable accommodation. I booked a place in Airbnb for mine so not only did I get trained with Galaxy server administration but I also had a first-hand information about the city from a local. I stayed in 2 different places: somewhere in Blindern during the entire workshop and another one in Rosenborg (close to the city center) for the weekend before my flight back to Dublin.

View from my Airbnb flat in Blindern

The sky was clear and the sun was out on our first day of training. Our instructors, who came from different parts of the world were also the main code contributors to the Galaxy project so everyone was enthusiastic to learn from them.

Our training jumpstarted with modules on how to install and deploy Galaxy program via PostgreSQL and nginx databases and basic pre-requisites or dependencies for running the server. We were also taught how to further extend Galaxy installation and customize our “brand” to what we need the server for.

The event organizers arranged a get-together dinner for us the next day. We went to Cafe Elias Mat & Sant in the city center and had traditional Norwegian dishes: my favorite was the sautéed reindeer! I can’t stop thinking about the poor Rudolph the red-nosed reindeer though the entire time I was eating dinner. :/

Click to view slideshow.

The snow started falling hard come Wednesday yet we continued on with our training about the specifics of Galaxy server administration.

Snow-proof.

Even though we had to debug the scripts real-time and as we went along with the workshop, I have to say that our instructors were very keen with time and were very efficient in handling technical challenges. We discussed how to tailor fit the Galaxy configuration file and how to use Ansible to deploy the server.

Thursday was scheduled for us participants to deliver lightning talks. Some presented how to link a customized Galaxy server to a larger local (i.e. university) server and others talked about issues they encountered when uploading tools from different providers other than Tool Shed. Everyone had interesting new ideas and expressed their willingness to help address the difficulties raised. It was a very engaging day!

Taken from Galaxy Project news site: https://galaxyproject.org/galaxy-updates/2018-02/

Fast-forward to the last day of our workshop: we covered all the topics as scheduled and more! The instructors gave us additional tips and workarounds (that were not listed in the syllabus) on how to create and manage our own Galaxy server. Dr. Björn Grüning of Galaxy-Frieburg and Dr. Marius van den Beek of Curie Institute, Paris also demonstrated several ways to troubleshoot installation failures, Tool errors and non-running jobs in Galaxy. For all the modules presented, we always had a prepared exercise so the training was indeed hands-on.

We capped our very productive workshop by going to a bar and restaurant for a celebratory dinner by the harbor. People were playing BINGO when I got there which added to the already-celebrating atmosphere. One of my classmates won a box of essential oils for completing a round! Myself and one of the instructors almost won as well but we failed to shout “BINGO!” as soon as our last missing number was called so the prize was given to someone else! Ahh but it was fun! We all had a great time. 🙂

We all then took a walk and went back to our own quarters. Many of us had to fly back home the next day but I stayed for the weekend and visited some historical spots in the city. I also took Metro #1 and went all the way to the last station to spend a little time in the Winter Park before the sky turned pitch black again in the afternoon.

Click to view slideshow.

I flew back to Ireland the next day full of these exciting memories and new knowledge about Galaxy server administration.

I especially want to thank the Open Bioinformatics Foundation (OBF) Board for choosing me for their Travel Award and offering to defray the cost of this wonderful trip! More power to OBF!

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