UseGalaxy.no updates

2025-12-10

• The Galaxy server has been upgraded to version 24.0

2025-12-09

• The Galaxy server was taken down and physically moved to a new room

2025-10-31

• We have set up a new CVMFS server to host the "data.usegalaxy.no" reference dataset repository, so those datasets that have been unavailable the last few weeks should now be back again (including datasets related to Salmon and Sea Lice).

2025-09-26

• There have been some problems running jobs recently due to issues related to SSH certificate renewal on our database server. This should have been fixed now.

2025-07-08 and 2025-07-09

• The PostgreSQL database server was upgraded from version 10 to version 15.

2024-12-02

• The UseGalaxy.no server is finally up again after a long downtime where we had to fix many problems.

2024-11-15

• The hypervisor running three of the virtual machines for UseGalaxy.no was taken down to perform routine maintenance work. Unfortunatey, when we tried to start up the servers again afterwards, it was discovered that the disk partitional table was corrupt. The user data was not affected, but the problem prevented us from starting up Galaxy. Fixing the issue turned out to be much harder than initially anticipated.

2024-06-18

• The CPU and memory allocation for the BlastN tool was been downscaled to improve resource utilization when running small queries against FASTA files from histories. This will allow more BlastN jobs to run concurrently and frees up resources that the tool will not be able to use anyway. However, the performance may be negatively impacted for BlastN searches against pre-built databases. If you find that this choice has unfortunate consequences for you, please contact our administration team.

2024-04-11

• We have now solved the problem with the "/tmp" location which affected several tools, including e.g. FastQC
• The T-Coffee multiple sequence alignment tool has also been fixed (Galaxy Version 13.45.0.4846264)

2024-04-03

• The UseGalaxy.no server has been upgraded to version 23.2   [ Read more ]

2024-03-14

• The problems with our "slurm.usegalaxy.no" compute node have finally been fixed, and the node has been brought back into our cluster

2024-02-07

• Fixed the tool Convert genome coordinates (aka "liftover")

2024-01-03

• Fixed the tool Calculate protein properties

2023-10-27

• Fixed the tool CD-HIT (Galaxy version 1.2). It now runs with CD-HIT 4.8.1 instead of 4.6.1
• Increased memory quota for ClustalW from 4GB to 34GB

2023-10-25

• Installed latest version of Salmon (v1.10.1)

2023-09-15

• Replaced an old, non-functional version of the InterProScan tool with a new version that works. Also installed InterPro database 5.59-91.0
  Note that the three licensed tools Phobius, SignalP and TMHMM are not installed and will lead to an error if selected.

2023-09-11

• Increased memory for the tool Blast Reciprocal Best Hits from 4GB to 20GB

2023-08-21

• Fixed the tool Blast Reciprocal Best Hits and replaced version 0.1.11 with 0.3.0
• Fixed the tool MLST so it does not break if the "Output novel alleles" option is selected but no novel alleles are found

2023-08-21

• Fixed the tool Protein Database Downloader (v0.3.4)

2023-08-17

• The Galaxy server went down on August 17th because the disk containing the database was full. The problem was fixed the following day.

2023-07-10

• Fixed the tools:
  • IEDB MHC Binding prediction
  • Unipept retrieve taxonomy for peptide (versions 4.0.0 and 4.3.0)
  • Get sequences by Ensembl ID using REST API

2023-05-30

• New tools:
  • Kraken-biom
  • Phyloseq suite:
    • Create phyloseq object from dada2 sequence and taxonomy tables
    • Phyloseq: plot alpha diverstiy measure
    • Phyloseq: plot ordination

2023-05-26

• Fixed the tools
  • QualiMap BamQC
  • SnpEff to Peptide fasta
  • NCBI Accession Download (upgraded to working version 0.2.8. Older versions were removed)
  • UniProt ID mapping and retrieval (upgraded to version 0.4. Older versions were removed)

2023-05-24

• Support for interactive tools – including Jupyter – has now been disabled on UseGalaxy.no. (They never worked properly anyway.)
  We hope to bring these back in the future. But, due to limited manpower, this will not be a priority.

2023-05-09

• Fixed some problems with the Kraken database "Bacteria (locally cached. Should be faster)" so it should now work with related Kraken tools also (like Kraken taxonomic report)

2023-05-05

• Increased the number of cores available to the tools Kraken and Kraken2

2023-04-21

• Fixed the tools
  • Faster Download and Extract Reads in FASTQ format from NCBI SRA (Galaxy Version 2.11.0+galaxy1)
  • Download and Extract Reads in FASTA/Q format from NCBI SRA (Galaxy Version 2.11.0+galaxy0)
  • Older versions of the same tools were removed

2023-04-14

• Fixed the tools MAF to FASTA, MAF to Interval and Extract MAF by block number (and perhaps some other MAF tools as well).

2023-04-13

• The connection to NeLS Storage, which was broken after migration to a new storage server before Easter, has been restored.

2023-04-11

• Fixed the problems that have caused all jobs to fail since April 8.
• The options to import/export histories between UseGalaxy.no and the NeLS Storage have been removed from the bottom of the history options menu (cogwheel button). To transfer histories, please use the approach described here instead.

2023-03-09

• Increased memory quotas for the tools Kraken and Kraken2

2023-02-23

• Installed 13 tools in the HUMAnN tools suite version 3.6.0 with reference data.
  Please note that there are other tools already available with near identical or similar names that refer to "HUMAnN2" rather than just "HUMAnN", but those are for an older version of HUMAnN.
  • HUMAnN
  • Barplot stratified HUMAnN features
  • Join (merge) gene, pathway, or taxonomy HUMAnN/MetaPhlAn tables into a single table
  • Make strain profiles
  • Normalize combined meta'omic sequencing data
  • Perform metadata association on HUMAnN generated table
  • Reduce a joined HUMAnN table
  • Regroup HUMAnN table features
  • Rename features a HUMAnN generated table
  • Renormalize a HUMAnN generated table
  • Split a HUMAnN table into 2 tables (one stratified and one unstratified)
  • Split a merged HUMAnN table
  • Unpack pathway abundances to show the genes for each

2023-02-22

• Installed tool MetaPhlAn version 4.0.3 with database "mpa_vJan21_CHOCOPhlAnSGB_202103".
  Please note that the tool named "MetaPhlAn2" refers to an older version whereas the tool just named "MetaPhlAn" refers to this newer version.
• Fixed the tools SortMeRNA (version 2.1b) and Export to GraPhlAn

2023-02-21

• Fixed the Cactus whole-genome multiple sequence alignment tools
• Removed the tool Fetch taxonomic representation, since it was not working properly

2023-02-03

• Due to problems with Singularity, all jobs running on our ecc3 compute node lately have failed with the error "Failed to create user namespace: user namespace disabled". This has now been fixed!

2023-01-20

• New tools:
  • BaSiC Illumination installed in the Multiplex Tissue Imaging section
• CPU and memory quotas have been increased for Cutadapt and all Multiplex Tissue Imaging tools

2023-01-09

• CORS has been enabled for external display applications, including Avivator

2022-12-13

• New tools have been installed in the Multiplex Tissue Imaging section:
• ASHLAR
• Convert McMicro Output to Anndata
• Gate Finder
• Mesmer
• MCQUANT
• Single Cell Phenotyping
• Spatial Analysis Tools
• Squidpy Graph and Plotting
• s3segmenter
• UNetCoreograph
• UnMicst
• Vitessce Visualization

2022-12-12

• Installed new tool: GenomeScope

2022-12-09

• Upgraded the following tools in the Salmon suite to version 1.9.0+galaxy2
• Salmon quant
• Salmon quantmerge
• Alevin