Upcoming Server Migration

November 7, 2018 Freiburg devops

We will be migrating Galaxy to new hardware. The hardware acting as the ‘head node’ is reaching End-of-Life and needs to be decomissioned.

Training Infrastructure Feedback from Maria Doyle

October 31, 2018 Freiburg training tiaas

We recently had the privilege of using the usegalaxy.eu’s new Training infrastructure as a Service (TIaaS) for our course on “Introduction to Galaxy and RNA-seq” at the Peter MacCallum Cancer Centre in Melbourne, Australia. Our own infrastructure was undergoing an upgrade and our planned workshop was going to be delayed but thanks to the TIaaS we were able to go ahead and run our workshop. All went smoothly and the feedback was very positive with 100% saying they would recommend the course to colleagues. A big thanks to the Galaxy EU team for providing this great resource.

“Selbst ist der Forscher: Big-Data-Analysen leicht gemacht”, a new German article written by The Freiburg Galaxy Team about our service and our work was published in the Laborpraxis.

Heinz is an algorithm for searching an optimal subnetwork from a bigger network. It can be applied to biological networks like gene regulation and protein-protein network to pinpoint the subnetwork of interest. We are pleased to announce that Heinz tools have been integrated into the Galaxy platform and are available on our server.

The Galaxy community is developing and maintaining a collection of tutorials that are designed to be interactive and are built around Galaxy: https://training.galaxyproject.org. To help highlight our tutorials and the training effort of the community, a member of the community will select every month one tutorial and explains in the Galactic Blog why they select this tutorial. This month, the Galaxy contributor of the Month!, Yvan Le Bras, selects and presents a tutorial: “Galaxy 101”, from the topic “Introduction to Galaxy Analyses”

“Datenanalyse mit dem Galaxy Server”, a German article written by The Freiburg Galaxy Team about our service and our work was published in the Laborjournal.

Initial release of `gxadmin` tool

October 8, 2018 Freiburg devops

We have recently released a small utility we use for helping manage our Galaxy server. It is available on GitHub and includes many small SQL queries that administrators run every day.

The Galaxy community is developing and maintaining a collection of tutorials that are designed to be interactive and are built around Galaxy: https://training.galaxyproject.org. To help highlight our tutorials and the training effort of the community, a member of the community will select every month one tutorial and explains in the Galactic Blog why they select this tutorial. This month Maria Doyle has selected the tutorial “From peaks to genes”, from the topic “Introduction to Galaxy Analyses”.

A successuful Galaxy HTS data analysis workshop

September 24, 2018 Freiburg training

A new Galaxy workshop on HTS data analysis was held in Freiburg last week.

UseGalaxy.eu Downtime

September 21, 2018 Freiburg devops downtime

We had a confluence of unexpected and bad events which resulted in UseGalaxy.eu offline for a significant portion of yesterday (2018-09-20) afternoon. No data was lost.

The Freiburg Galaxy Team is looking for a JavaScript developer.


July 18, 2018 Freiburg training

From 24th of June to 2nd of July the Galaxy Community Conference (GCC) and Bioinformatics Open Source Conference 2018 (BOSC) were meeting together in Portland, Oregon, United States. There was be two days of training, a two day meeting, and four days of intense collaboration. The meeting featured joint & parallel sessions, shared keynotes, poster & demo sessions, birds-of-a-feather, and social events. Bérénice, Joachim, and Björn were there and represented the Galaxy Freiburg team!

Temporarily Held Workflow Invocations

July 12, 2018 Freiburg devops downtime

Users reported workflows were not running, we investigated and could not find the root cause but did solve the issue.

3 years ago the Galaxy community evaluated mechanism to make software installation more robust and we joined the Bioconda community, to fix the software deployment problem once and for all. Today, we are happy to annouce that the Bioconda manuscript is now published in the latest Nature Methods issue (public view). usegalaxy.eu and many other Galaxy instance are already powered by Bioconda and you might use it daily without knowing :)

HiCExplorer - a tool suite for reproducible Hi-C data analysis, quality control and visualization was published a few days ago.

Carolin Rommel, from the Institute of Experimental and Clinical Pharmacology and Toxicology, recently published her manuscript about “The Transcription Factor ETV1 Induces Atrial Remodeling and Arrhythmia”. Great work, congratulations Carolin!

Tool Usage Graphs

July 3, 2018 Freiburg devops

We have leveraged the Galactic Radio Telescope to produce graphs of tool usage over time. You can embed these anywhere, in websites, in tool forms, etc.

Database outage affecting UseGalaxy.eu

June 18, 2018 Freiburg devops downtime

Our database server crashed unexpectedly on friday night and we were down over most of the weekend.

Data Carpentry workshop and CarpentryCon

June 6, 2018 Freiburg training talk

Last week was CarpentryCon at University College Dublin, Ireland.

From 21st to 23rd of May was held a workshop for Galaxy training material and skills improvement at the Earlham Institut in Norwich. Bérénice and Björn were there!

Temporary Quota Issue

June 4, 2018 Freiburg devops downtime

We had a temporary quota issue today when one of our developers working on automating UseGalaxy.eu Quota Increase Application made a mistake in the code which resulted in the legacy-users quota membership being removed.

Nanopolish is a popular tool suite for working with data produced by the Nanopore sequencing platform. We are pleased to announce that the demanding tools have been integrated into the Galaxy platform and are available on our server.

The Galaxy project has published an 2018 update of the core Galaxy framwork with all the new features of the last two years. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update.

UseGalaxy.eu update to 18.05 and GDPR

May 25, 2018 Freiburg release

We’ve updated our Galaxy server to version 18.05. Additionally we have enabled the beta_gdpr_mode that the Freiburg Galaxy Team implemented in Galaxy.

In memory of Christophe Caron

May 7, 2018 Freiburg

It’s with incredible sadness that we need to notify you that Christophe Caron passed away. He suffered a heart attack during a football game last Friday.

DNS outage affecting UseGalaxy.eu

April 26, 2018 Freiburg devops downtime

Google’s DNS stopped responding to requests for usegalaxy.eu for 35 minutes.

Fileserver Outage affecting Jobs

April 24, 2018 Freiburg devops downtime

The university’s home directory server went offline affecting numerous Galaxy jobs.

New Galaxy Team member!

April 23, 2018 Freiburg galaxyteam

The Galaxy Team in Freiburg has a new member.

Galaxy Workshop registration open!

April 18, 2018 Freiburg training

The registration for our next Galaxy Workshop on HTS data analysis from 17-21 September 2018 in Freiburg is open. We have 30 places. More information can be found in events on our homepage. Participants are selected from the applicants. Apply now!

Galaxy Africa

April 11, 2018 Freiburg training talk

The first Galaxy conference was held last week in Africa, organized by SANBI at University of Wester Cape in Cape Town. Björn and Bérénice participated:

The Galaxy User Conference in Freiburg just ended!

Freiburg Galaxy becomes useGalaxy.eu

March 15, 2018 Freiburg devops

As part of our ongoing growth and development, Freiburg Galaxy is becoming useGalaxy.eu

More than 120 participants joined us for the first Galaxy User Conference in Freiburg. The first day has just ended and what an amazing day it was!

The ELIXIR Galaxy community kick-off meeting was held here in Freiburg.

Propagating hashtags in a Galaxy history

March 9, 2018 Freiburg galaxy tools users software-release

We have written a utility to help you propagate tags through your histories. Did you forget to tag the inputs before running a long workflow? We’ve now solved this issue.

The MiModD suite of tools, developed in the Baumeister lab at the Institute for Biology 3 here in Freiburg, is now available on the server. MiModD is for geneticists who have isolated phenotypic mutants of their favourite organism, e.g., through forward genetic screens, and who now wish to map the underlying mutations and eventually identify them molecularly.

deepTools3 is now available!

March 3, 2018 Freiburg tools

The deepTools developers have released a brand new version! This time with CRAM support, new normalization and plotting options, new tools, e.g. alignmentsieve for ATAC-seq, and many more.

We are happy to announce that we are hosting the ELIXIR Galaxy community kick-off meeting here in Freiburg. ELIXIR members meet at 14.03.2018 starting from 13:00 at the technical faculty of the University of Freiburg. Everyone is invited to join, but please let us know so that we can plan accordingly. More information you can found here.

Program for the Galaxy User Conference

February 13, 2018 Freiburg

Our preliminary program for the Galaxy User Conference is now ready. You can fine more information here and register here.

Genome Annotation Reloaded

February 11, 2018 Freiburg tools

During the last month the Galaxy team has put a lot of effort into updating the Genome Annotation tools and has included new tools that will change how you work with your Genome in silico.

Clemens and the GalaxyP team have published a new article about metaproteomics and Galaxy. [Learn more about it](https://www.mdpi.com/2227-7382/6/1/7).

Because many people already asked: The autumn Galaxy Workshop on high-throughput data analysis will take place from 17.-21.9.2018 here in Freiburg. Registration will be open from mid of April 2018 on. Save the date!

Galaxy Workshop - Registration is closed!

January 18, 2018 Freiburg training

Due to the high number of applicants for the next Galaxy workshop from 26.02.-02.03.2018, we close the registration. Participants will be selected from the applicants until 02.02.2018. The next workshop will take place in September 2018.

The Freiburg Galaxy Team is looking for 2 Postdoctoral researchers.

New generation of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies.

New manuscript by Fidel Ramirez et al. about “High-resolution TADs reveal DNA sequences underlying genome organization in flies” was published today. Want to learn HiC data analysis? Try HiCExplorer in your tool menue!

“Combinatorial omics analysis reveals perturbed lysosomal homeostasis in collagen VII-deficient keratinocytes” by Kerstin Thriene et al. was published today in Molecular and Cellular Proteomics. Thanks to Kerstin, Jörn and Collegues for this great collaboration.

ELIXIR Galxy Admin workshop in Oslo.

January 12, 2018 Freiburg training

We had a very nice Galaxy Admin workshop in Oslo.

Post Mortem: 2h Tool Execution Outage

December 11, 2017 Freiburg devops downtime

Today (2017-12-11) we had a temporary outage of job executions. We’ve been making progress on a new job configuration system for our Galaxy which should let us reconfigure job scheduling in a more dynamic way. After weeks of work and testing we’re finally rolling this out to 6% of our users. Unfortunately as part of the deployment we failed to install two dependencies that were required as part of the new changes.

Bioinformatic training with the B3Africa project

December 10, 2017 Freiburg training

Tomas Klingström from the Swedish University of Agricultural Sciences and part of the amazing B3Africa project used the Freiburg Galaxy server for this training last week. Read his guest post here:

Our paper “Community-driven data analysis training for biology” about the Training material we are developing with the Galaxy Training Network is now available as preprint on bioRXiv.

Congrats to Douglas M. Lopes, et. al from the Franziska Denk group at King’s College London for their new paper Sex differences in peripheral not central immune responses to paininducing injury.

Congrats to Stephan Nothjunge, Thomas Nührenberg, Ralf Gilsbach and many more from the Hein group for their new paper entiteled DNA methylation signatures follow preformed chromatin compartments in cardiac myocytes.

Post Mortem: Upload and various tool failures

November 21, 2017 Freiburg devops

Yesterday (2017-11-20) all upload jobs and some other tools were failing to be launched on our cluster. One of our clusters became unresponsive and the code which handled job distribution to clusters had to be updated. This process required three iterations to get correct. Each update cycle took ~15-20 minutes due to our update process and how long it takes Galaxy to switch over to the new configuration.

We are offering another Galaxy workshop on HTS data analysis. Please apply here.

Successful Server Hardware Improvements

November 15, 2017 Freiburg devops

Last wednesday we had a short, 1-hour maintenance period during which we upgraded the memory of the Galaxy head node. It was originally sitting at 32Gb of RAM but we ran into numerous issues handling the volume of jobs that are launched every day. We have since upgraded to 64Gb and performance has been smoother.

Galaxy 17.09 released!

November 8, 2017 Freiburg release

We just updated our Galaxy server to version 17.09! Actually this was done by H. Rasche, our new team member! Welcome Helena!

90+ tools updated

November 8, 2017 Freiburg tools

We updated our tools stack - more than 90 tools were updated to newest versions!

Do you have Nanopaore or PacBio reads? Try minimap2 as a new aligner! From minimaps homepage:

First imaging mass spectrometry added

November 2, 2017 Freiburg tools

Thanks to a contribution from Melanie Föll (Schilling Lab) we have added tools for analysing imaging mass spectrometry data.

Latest version of MultiQC

October 25, 2017 Freiburg tools

MultiQC is a tool that aggregate results from bioinformatics analyses across many samples into a single report. It is really a great and useful tool!

Joachim presented the developments of HiCExplorer at the 5th early-stage researchers Next-Generation Sequencing Symposium in Heidelberg.

During the de.NBI Symposium 2017, Bérénice presented the poster “Building an open, collaborative, online infrastructure for bioinformatics training”.

Our paper about BioConda on bioRXiv

October 21, 2017 Freiburg paper

Our paper “Bioconda: A sustainable and comprehensive software distribution for the life sciences”, written with the great and big BioConda community, is now available as preprint on bioRXiv.

Bérénice was helping Toby Hodges, Malvika Sharan and the other instructors for the Software Carpentry workshop organized at EMBL in Heidelberg.

MetaboFlow meeting (training and hackathon)

October 17, 2017 Freiburg training hackathon

Björn participated to the Wellcome Trust funded MetaboFlow meeting (training and hackathon) in Birmingham.

Our paper “Practical computational reproducibility in the life sciences”, written with Johannes Köster, Ryan Dale and several members of the US Galaxy team, is now available as preprint on bioRXiv.

BioContainer Hackathon

October 10, 2017 Freiburg training hackathon

Björn, Yasset Perez-Riverol (EBI), and the French ELIXIR node organised a BioContainer Hackathon in Paris.

We have been experimentally running some Galaxy jobs in the bwCloud at the University of Freiburg. Unlike more traditional compute resources we can scale the cloud resources up and down on-demand.

Björn was at the deNBI Summer School on Computational genomics and RNA biology organised by the RNA Bioinformatics center. He gave training on:

FIXED: upload jobs not scheduled

September 28, 2017 Freiburg devops

A subset of upload jobs were hanging. Investigation pointed to a handful of VMs that were recently launched in our cloud which were firewalled off from access. Condor, our job scheduler, needs to be able to reach the VMs in order to send jobs to it. When jobs were scheduled for those VMs, they just hung indefinitely. We have now corrected the issue in code, so we won’t launch any more VMs with this issue.

After 5 days, our HTS Galaxy workshop in Freiburg is over.

3 Galaxy related posters @ GCB 2017

September 20, 2017 Freiburg poster

During the German Conference on Bioinformatics in Tübingen, we presented (with Milad Miladi) 3 posters related to Galaxy:

We passed the 2.000.000th job!

September 14, 2017 Freiburg jobs

Today our Galaxy server has calculated its 2.000.000th job! Thanks to all our users and people that have contributed to this project!

Fixed: Galaxy Metadata Issue

August 31, 2017 Freiburg devops

Many of you have noticed issues setting metadata recently. We had implemented a change with the hopes of fixing a bug we were seeing, however it had the unfortunate effect of causing most metadata setting jobs to fail.

Search and get data from ENA with ENASearch

August 31, 2017 Freiburg tools

We added to the instance ENASearch, a tool for interacting with ENA’s API. It allows you to search and retrieve data from ENA directly inside Galaxy.

STAR: Ultrafast alignment of RNA-seq data

August 2, 2017 Freiburg tools

For the mapping of non-contiguous transcripts, this program was developed. STAR’s speed and reliability have been proven. The mapper was recently updated on this server and several often used reference genomes are already online.

Talks, poster and training @ ISMB and BOSC

July 23, 2017 Freiburg training talk poster

Björn and Bérénice were participating to ISBM/ECCB 2017 and particularly to Bioinformatics Open Source Conference (BOSC)) (satellite of ISBM/ECCB):

W4M: Workflow4Metabolomics 3.0

July 2, 2017 Freiburg tools

Our friends from Workflows4Metabolomics have updated there tools and workflows to version 3.0 - and so did we. Enjoy all the great new tools dedicated to metabolomics data processing, analysis and annotation for Metabolomics community.

Galaxy Community Conference (GCC)

June 30, 2017 Freiburg training talk poster

Clemens, Björn and Bérénice were participating in the Galaxy Community Conference GCC training: