TIaaS Queue Status

June 17, 2019 Freiburg devops

A common request during trainings was “how are the students doing, are they finished with the current step?” This is a common question, especially given some of the sleepy grad students trainees at 9am. For our TIaaS users, we have added a brief overview of the training queue, showing them at a glance if everyone is finished with the current step.

UseGalaxy.eu Tool Updates for 2019-06-15

June 15, 2019 Freiburg tools

On 2019-06-15, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build #108

As of Galaxy version 19.05 released last month, Galaxy can easily be configured to use Elixir-AAI service for authenticating users! As the first publicly available Galaxy instance, the European Galaxy Server hosted by Elixir Germany is now ready to accept logins from users using their Elixir AAI identity for authentication.

Training Infrastructure Feedback from Nevena Veljkovic

June 10, 2019 Freiburg training tiaas

In the spring semester, the Molecular Biology, a three-year PhD programme by the Faculty of Biology in Belgrade offered an elective course Genomics. This year 7 students attended this course.

UseGalaxy.eu Tool Updates for 2019-06-08

June 8, 2019 Freiburg tools

Tool Updates

UseGalaxy.eu update to 19.05

June 6, 2019 Freiburg release

We’ve updated our Galaxy server to version 19.05 and now use EU blue in celebration of European Unity, ahead of us hosting this year’s Galaxy Community Conference

UseGalaxy.eu Tool Updates for 2019-06-06

June 6, 2019 Freiburg tools

On 2019-06-06, the tools on UseGalaxy.eu were updated by our automated tool update and installation process in Jenkins Build 106

Queue changes during GCC

May 24, 2019 Freiburg devops

As Freiburg is hosting the Galaxy Community Conference this year, we will be allocating a lot of extra resources for training and events during the conference. To accomplish this, we will decrease the size of the main queue, and re-allocate these resources to the conference. You may notice that jobs take longer to run in the weeks before/during/after the conference, please be patient with us during this time. After the conclusion of the conference things will return to normal.

Another successful Galaxy workshop in Melbourne

May 20, 2019 Freiburg training tiaas

Recently we ran another Galaxy workshop using UseGalaxy.eu’s Training infrastructure as a Service (TIaaS). The workshop was an “Introduction to Galaxy and RNA-seq” run over two afternoons at the Peter MacCallum Cancer Centre in Melbourne, Australia. The attendees were a mix of students and postdocs and their feedback was good, they liked the hands-on, practical nature of the course. Thanks to the Galaxy EU team for enabling the course through providing the convenience of the TIaaS service.

Galaxy Workshop registration open!

May 10, 2019 Freiburg training

The registration for our next Galaxy Workshop on HTS data analysis from 23-27 September 2019 in Freiburg is open. We have 30 places. More information can be found in events on our homepage.

A new significant update of our RNA workbench was released! You can access the new tools, workflows, tours and tutorials at http://rna.usegalaxy.eu/. Check out our new paper to get more information.

Last week, the ELIXIR Galaxy Community organized a 4-days workshop related to Galaxy tool integration and training. This event was hosted by the Biological station of Roscoff, in the (sunny/rainy) beautiful Brittany (France).

GCC2019 will be held 1-8 July in Freiburg, Germany. The tenth GCC will have many familiar features from earlier years, including accepted and lightning talks, posters and demos, birds-of-a-feather gatherings (BoFs), training, and a CollaborationFest. 2019 also brings the most significant conference program update in several years! Find out more on the event page.

Recently, we have started working with the Macromolecular Crystallography group, which is based at the Diamond synchrotron in Didcot, UK. We have a common interest in enabling reproducible, user-friendly data analysis in cheminformatics and computational chemistry. As part of their XChem project, they are developing computational workflows to assist in designing follow-up compounds from fragment screening hits. Diamond is working with Informatics Matters to develop Squonk, a computational notebook with similar aims to the ChemicalToolbox we are working on. We were interested in investigating how Squonk and Galaxy could be integrated.

UseGalaxy.eu Tool Updates for 2019-04-23

April 23, 2019 Freiburg tools

Tool Updates

FASTQC jobs and very long reads

April 14, 2019 Freiburg devops tools

Over the past few weeks we saw many FASTQC jobs running for days or even longer, which is not normal. We investigated this and saw that all of those jobs are processing files with unusually long reads.

UseGalaxy.eu Tool Updates for 2019-04-06

April 6, 2019 Freiburg tools

Tool Updates

As you probably know GCC2019 will be held in Freiburg, Germany, from 1-6 July. Like previous Galaxy Community Conferences, GCC2019 will feature keynotes, accepted talks, posters, and demos, birds-of-a-feather gatherings, multiple days of collaborative work, and plenty of opportunities to network with your fellow data-intensive researchers and practitioners. If you are working in data-intensive life science, there is no better place to be.

This week we are celebrating 5 million jobs and 5 thousand users. Since we opened the Galaxy server to the public a year ago we got 4000 new users and every 2 minutes a job finishes. This would not be possible without the support of de.NBI, ELIXIR, EOSC and the Freiburg Faculty of Medicine.

msconvert is a tool to convert mass spectrometry data file formats.

UseGalaxy.eu update to 19.01

March 19, 2019 Freiburg release

We’ve updated our Galaxy server to version 19.01.

UseGalaxy.eu Downtime on 18th March

March 18, 2019 Freiburg devops downtime

A normal upgrade went awry and we had to restore some data from backup. We had a total downtime of around 20 hours.

In collaboration with our cooperation partner at the Scientific Computing Research Unit, University of Cape Town, we have recently published “Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE)”. This publication provides a basis for performing molecular dynamics simulations and analysis through Galaxy, using a number of commonly used packages, such as NAMD, GROMACS and CHARMM (for simulation) and Bio3D and MDAnalysis (for analysis).

New Paper The Chimera and the Cyborg

March 14, 2019 Freiburg paper

Our admin Helena, in collaboration with the Rechenzentrum Uni Freiburg, has published “The Chimera and the Cyborg: Hybrid Compute: In vivo HPC, Cloud and Container Implementations”.

Galactic News

March 5, 2019 Freiburg galaxy

Find a summary of what is going on in the Galaxy community in March 2019.

Last week, the Freiburg Galaxy team taught a 5 day workshop on HTS data analysis in Freiburg!

Our paper “Empowering the annotation and discovery of structured RNAs with scalable and accessible integrative clustering” is now available as preprint on bioRXiv. Congratulation to Milad and co-authors!

Tool Quest: Do you know the answer?

February 9, 2019 Freiburg training

Last week we got a request from on of our users with a tricky question:

The Galaxy Community Conference starts with training but also continues with training throughout the conference. The community proposed some topics and now you need to vote to select the ones offered at GCC2019! Please take a few minutes to vote which ones should be offered at GCC2019! Thank you!

Learn how the NASA uses Galaxy!

January 26, 2019 Freiburg training

Dave B pointed us to this nice article about “Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform”.

GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. A tutorial for the tool is also available at the Galaxy Project training website.

This semester, the Faculty of Biology at the University of Belgrade offered for the first time an elective master course Introduction to Genomics which included several hands-on sessions on the Galaxy platform.

A successful Galaxy RNA-seq workshop in Belgrade

January 19, 2019 Freiburg training

Last week, the Freiburg Galaxy team taught a 2 day course in the beautiful city of Belgrade!

Queue cleared

January 18, 2019 Freiburg devops downtime

We had to clear the queue due to an emergency today. We had noticed that a filesystem was extremely slow around 2 days ago, and had updated our Galaxy configuration to work around this. Unfortunately we failed to restart the handlers so new datasets continued to be written to that path, until the point at which it became an emergency and the system became completely unresponsive.

Another European CVMFS mirror is online

January 11, 2019 Freiburg devops

The CernVM File System (CVMFS) provides a scalable, reliable and softare and data distribution service. It was originally developed to assist High Energy Physics (HEP) collaborations to deploy software on the worldwide-distributed computing infrastructure used to run data processing applications. The Galaxy project is using the same technology now to distribute 6TB of reference data and Singularity images to the scientific community. This will make analysis more reproducible across Galaxy instances as the reference data is also shared. However, the provided data can be used without Galaxy and for example will be available inside the de.NBI cloud.

Galaxy HTS Workshop 25.2.-1.3.2019 - fully booked

January 10, 2019 Freiburg training

Our next Galaxy Workshop on HTS data analysis from 25.2.-1.3.2019 in Freiburg is full. However, you can assign yourself to our waiting list.

The European Galaxy Team is hiring!

New hardware: 8x1TB memory nodes

January 8, 2019 Freiburg devops release

Today we activated our brand new hardware. Thanks to the Federal Ministry of Education and Research we could extend the de.NBI-Cloud with 8x1TB nodes. This means more high-memory nodes for your memory intensive jobs, less waiting, faster results. Enjoy!

Maria Doyle has created a new tutorial about the visualization of RNA-Seq results with Volcano plots.

Gajan Kristnaskon kaj bonan novjaron!

December 25, 2018 Freiburg devops

We all wish you a Merry Christmas and a Happy New Year. Enjoy the holiday season with your family and see you all next year. Our dear friend Martin Čech summed it up nicely :)

Automatic resubmission of failed Galaxy jobs

December 19, 2018 Freiburg devops

UseGalaxy.eu has now started automatically resubmitting any jobs which fail.

UseGalaxy.eu update to 18.09

December 11, 2018 Freiburg release

We’ve updated our Galaxy server to version 18.09. Everything went extremely smoothly.

The 2019 Galaxy Community Conference (GCC2019) will be held in be held in Freiburg, Germany, 1-6 July. The training topics that are offered are determined by the community so BY YOU!

BeerDEcoded: unofficial kickoff

November 30, 2018 Freiburg training

Street Science community aims to make science tangible & accessible by bringing it to the “street” via open science workshops. In November, we had an unofficial kickoff of the BeerDEcoded project: we poured Beer into the MinION’s pores: sequencing yeast extracted from Beer with Nanopore.

European Galaxy Days

November 26, 2018 Freiburg training

European Galaxy Days were held 19 and 20 November 2018 in Freiburg, Germany. >40 participants from all Europe and even US meet for this two day gathering.

ELIXIR Biohackathon in Paris

November 23, 2018 Freiburg training

ELIXIR France with the support of the ELIXIR Hub and the ELIXIR interoperability platform and in collaboration with COST CHARME, the National Bioscience Database Center (NBDC) and the Database Center for Life Science (DBCLS), organized last week (November 12th - 16th, 2018) a BioHackathon in Paris. Bérénice, Helena, Björn, and Saskia were there and represented the Galaxy Freiburg team and ERASMUS MC. The event was a total blast: 5 days in a remote area to work, code, have fun, eat and discuss with the 150 other participants from all Europe (even US)!

Automatic workflow testing

November 21, 2018 Freiburg devops

We have started to test a few of our workflows automatically against UseGalaxy.eu. This will run all workflows monthly to ensure that the keep working and that our infrastructure works and scales well.

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!, Saskia Hilteman, selects and presents a tutorial: “Reference-based RNA-Seq data analysis”, from the topic “Transcriptomics”

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.

An ELIXIR-NL training course entitled Bioinformatics for Translational Medicine using Galaxy: see it, do it, teach it! was held on October 17 - 19, 2018 in Amsterdam. Participants were enthusiastic about the course contents, and particularly interested in the link of using Galaxy workflows for training and teaching. For this workshop we used the European Galaxy server via their wonderful Training Infrastructure as a Service (TIaaS) setup.

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”.

Cloud Migration Postmortem

September 26, 2018 Freiburg devops downtime

The bwCloud which we relied on for cloud hosting has reach end of life, and is being replaced with bwCloud SCOPE. This documents our migration between the two clouds.

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.

GCCBOSC

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.

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.

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!

Updated PhageTerm

March 14, 2018 Pasteur devops

We have updated PhageTerm to version 1.0.11

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.

Melanie and colleagues published a paper on “Reproducible proteomics sample preparation for single FFPE tissue slices using acid-labile surfactant and direct trypsinization”. Thank you for using Galaxy and congratulation to the authors!

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!

Updated Salmonella CRISPR Typing

January 26, 2018 Pasteur devops

We have updated Salmonella CRISPR Typing to version 1.0.1 CRISPR Typing.md

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:

Updated multiqc

November 30, 2017 Pasteur devops

We have updated multiqc to version 0.7.0

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.

We have updated Generate readmap and histograms from alignment files from sRbowtie aligment to version 1.2.0 readmap and histograms from alignment files from sRbowtie aligment.md

Updated Small RNA Signatures

November 24, 2017 Pasteur devops

We have updated Small RNA Signatures to version 3.1.0 RNA Signatures.md

Updated small_rna_maps

November 24, 2017 Pasteur devops

We have updated small_rna_maps to version 2.4.1

Updated DESeq2

November 23, 2017 Pasteur devops

We have updated DESeq2 to version 1.18.0

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.

Updated Fetch closest non-overlapping feature

November 17, 2017 Pasteur devops

We have updated Fetch closest non-overlapping feature to version 4.0.1 closest non-overlapping feature.md

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

Updated Get flanks

November 17, 2017 Pasteur devops

We have updated Get flanks to version 1.0.0 flanks.md

Updated Base Coverage

November 16, 2017 Pasteur devops

We have updated Base Coverage to version 1.0.0 Coverage.md

Updated Cluster

November 16, 2017 Pasteur devops

We have updated Cluster to version 1.0.0

Updated Complement

November 16, 2017 Pasteur devops

We have updated Complement to version 1.0.0

Updated Concatenate

November 16, 2017 Pasteur devops

We have updated Concatenate to version 1.0.1

Updated Coverage

November 16, 2017 Pasteur devops

We have updated Coverage to version 1.0.0

Updated Intersect

November 16, 2017 Pasteur devops

We have updated Intersect to version 1.0.0

Updated Join

November 16, 2017 Pasteur devops

We have updated Join to version 1.0.0

Updated Merge

November 16, 2017 Pasteur devops

We have updated Merge to version 1.0.0

Updated Subtract

November 16, 2017 Pasteur devops

We have updated Subtract to version 1.0.0

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.

Updated Salmonella CRISPR Typing

November 10, 2017 Pasteur devops

We have updated Salmonella CRISPR Typing to version 1.0.0 CRISPR Typing.md

Updated FASTQ to FASTA

November 9, 2017 Pasteur devops

We have updated FASTQ to FASTA to version 0.0.13 to FASTA.md

Updated Annotate smRNA dataset

November 8, 2017 Pasteur devops

We have updated Annotate smRNA dataset to version 1.1.1 smRNA dataset.md

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!

Updated Trinity

November 8, 2017 Pasteur devops

We have updated Trinity to version 2.2.0

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.

Updated Filter sequences by length

October 27, 2017 Pasteur devops

We have updated Filter sequences by length to version 1.1 sequences by length.md

Updated Pick Fasta sequences

October 27, 2017 Pasteur devops

We have updated Pick Fasta sequences to version 1.0.0 Fasta sequences.md

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!

Updated Normalize By Median

October 24, 2017 Pasteur devops

We have updated Normalize By Median to version 2.0.0 By Median.md

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.

Updated NCBI blast suite

October 20, 2017 Pasteur devops

We have updated NCBI blast suite to version 2.6.0 blast suite.md

Updated sR_bowtie

October 19, 2017 Pasteur devops

We have updated sR_bowtie to version 1.1.1

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

Updated cap3

October 17, 2017 Pasteur devops

We have updated cap3 to version 2.0.0

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.

Updated Get Fasta from BioMAJ

October 14, 2017 Pasteur devops

We have updated Get Fasta from BioMAJ to version 1.0.0 Fasta from BioMAJ.md

Updated Clip adapter

October 13, 2017 Pasteur devops

We have updated Clip adapter to version 2.0.1 adapter.md

Updated Oases_optimiser

October 13, 2017 Pasteur devops

We have updated Oases_optimiser to version 0.2.08

Updated Parse blast output and compile hits

October 13, 2017 Pasteur devops

We have updated Parse blast output and compile hits to version 2.4.3 blast output and compile hits.md

Updated Retrieve FASTA from NCBI

October 13, 2017 Pasteur devops

We have updated Retrieve FASTA from NCBI to version 2.0.0 FASTA from NCBI.md

Updated blast_to_scaffold

October 13, 2017 Pasteur devops

We have updated blast_to_scaffold to version 0.9.0

Updated fasta - tabular

October 13, 2017 Pasteur devops

We have updated fasta - tabular to version 1.1.0 - tabular.md

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:

Updated pindel2vcf

September 28, 2017 Pasteur devops

We have updated pindel2vcf to version 0.2.5a3

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.

Updated pindel

September 27, 2017 Pasteur devops

We have updated pindel to version 0.2.5a3

Updated growthpread

September 26, 2017 Pasteur devops

We have updated growthpread to version 1.07

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:

Updated macs2

June 16, 2017 Pasteur devops

We have updated macs2 to version 2.1.0

Updated dsrc

May 10, 2017 Pasteur devops

We have updated dsrc to version 2.0

Updated IGblast

April 28, 2017 Pasteur devops

We have updated IGblast to version 1.4.0

Updated STAR

March 16, 2017 Pasteur devops

We have updated STAR to version 2.5.0a

Updated featureCounts

March 16, 2017 Pasteur devops

We have updated featureCounts to version 1.4.6-p3

Updated Booster

March 1, 2017 Pasteur devops

We have updated Booster to version 0.1.12

Updated elp

February 20, 2017 Pasteur devops

We have updated elp to version 2.0

Updated xxr

February 20, 2017 Pasteur devops

We have updated xxr to version 3.03

Updated breseq

February 15, 2017 Pasteur devops

We have updated breseq to new visualisation

Updated phageterm

February 13, 2017 Pasteur devops

We have updated phageterm to 1.0.8

Updated capsuleFinder

February 7, 2017 Pasteur devops

We have updated capsuleFinder to version 1.0.2

Updated conjdb

January 26, 2017 Pasteur devops

We have updated conjdb to version 1.0.2

Updated TXSSCAN

January 24, 2017 Pasteur devops

We have updated TXSSCAN to version 1.0.2

Updated parsesnp

January 23, 2017 Pasteur devops

We have updated parsesnp

Updated blast2myDB

January 1, 2017 Pasteur devops

We have updated blast2myDB, workflow