Ubuntu 24 and software updates #27
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This PR updates the bioinformatics software versions, corresponding to a new AMI with these new versions installed (including upgrading R to 4.5.1). Previous AMIs for this lesson were successively upgraded in place from Ubuntu 14. The new AMI is based on a new Ubuntu 24 instance, with the lesson data added and conda environment rebuilt. No changes were necessary to the steps in the lesson.
Version upgrades:
Fastqc: 0.11.9 --> 0.12.1
Trimmomatic: 0.39 --> 0.40
Spades: 3.15.2 --> 4.2.0
CheckM-Genome: 1.2.1 --> 1.2.4
R: 4.2.1 --> 4.5.1
RStudio is also upgraded to the latest version.
Once it passes testing, this AMI will ultimately need to be copied to
N. Virginiaand the copy will be named to Carpentries' preferred name. The AMI name will need to be updated insetup.mdas well as_extras/AMI-setup.mdThe AMI to test is: ami-0cd0916e46475b1f9 which is located in the
United States (Oregon)AWS region. Recommend creating it ast3.largein order for the binning(?) step to have the 8GB memory that it needs.Please note the companion PR at: carpentries-lab/metagenomics-analysis#89