A major upgrade for Galaxy Australia server

May 22, 2018. 8:00 AM. We are doing a major upgrade on Galaxy Australia server. Among other things the upgrade will bring a new version of Galaxy and expand range of tools. Some old and obsolete tools will be replaced with new wrappers, eg the server will have new Trinity and SPAdes packages. Users will have to modify their workflows and replace the discarded tools with new versions. Re-run option does not work on datasets created with the discarded tools.

Some tools will have new versions available alongside with the older versions. In this situation the existing workflows and re-run option should work.

Some known issues.

Metadata has been lost on some old datasets. These jobs do not display correct settings with “Run this job again” option. The issue is known for some time and is not related to the upgrade.

HiSAT2 and RNA_STAR aligners do not assign database (genome assembly) to BAM files. At the moment users have to assign a correct database/genome assembly manually or through a Galaxy workflow. Note that BAM files without an assigned genome assembly cannot be displayed on UCSC Genome Browser and might be visualised on incorrect assembly with IGV.

Htseq-count (Galaxy Version 0.9.1)  fails with the default settings. It works with “Additional BAM Output” set to “Output additional BAM file” in the advanced settings.

On separate note, we cease all activities in this blog. A new platform for technical updates will be determined by our management at some point in the future.

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