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

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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.

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Genome Annotation Reloaded

Feb 11, 2018 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.

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Clemens and the GalaxyP team have published a new article about metaproteomics and Galaxy. Learn more about it.

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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!

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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.

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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.

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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!

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“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.

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Post Mortem: 2h Tool Execution Outage

Dec 11, 2017 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.

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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:

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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.

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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.

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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.

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

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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.

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90+ tools updated

Nov 8, 2017 tools

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

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Galaxy 17.09 released!

Nov 8, 2017 release

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

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

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

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Latest version of MultiQC

Oct 25, 2017 tools

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

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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.

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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.

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BioContainer Hackathon

Oct 10, 2017 training hackathon

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

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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.

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

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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.

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Fixed: Galaxy Metadata Issue

Aug 31, 2017 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.

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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.

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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.

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Galaxy Community Conference (GCC)

Jun 30, 2017 training talk poster