Ubuntu 24 and software updates

Gemfile

@@ -1,2 +1,4 @@
 source 'https://rubygems.org'
 gem 'github-pages', group: :jekyll_plugins
+
+gem "webrick", "~> 1.9"

Gemfile.lock

@@ -0,0 +1,263 @@
+GEM
+  remote: https://rubygems.org/
+  specs:
+    activesupport (6.0.6.1)
+      concurrent-ruby (~> 1.0, >= 1.0.2)
+      i18n (>= 0.7, < 2)
+      minitest (~> 5.1)
+      tzinfo (~> 1.1)
+      zeitwerk (~> 2.2, >= 2.2.2)
+    addressable (2.8.1)
+      public_suffix (>= 2.0.2, < 6.0)
+    coffee-script (2.4.1)
+      coffee-script-source
+      execjs
+    coffee-script-source (1.11.1)
+    colorator (1.1.0)
+    commonmarker (0.23.7)
+    concurrent-ruby (1.2.0)
+    dnsruby (1.61.9)
+      simpleidn (~> 0.1)
+    em-websocket (0.5.3)
+      eventmachine (>= 0.12.9)
+      http_parser.rb (~> 0)
+    ethon (0.16.0)
+      ffi (>= 1.15.0)
+    eventmachine (1.2.7)
+    execjs (2.8.1)
+    faraday (2.7.4)
+      faraday-net_http (>= 2.0, < 3.1)
+      ruby2_keywords (>= 0.0.4)
+    faraday-net_http (3.0.2)
+    ffi (1.15.5)
+    forwardable-extended (2.6.0)
+    gemoji (3.0.1)
+    github-pages (227)
+      github-pages-health-check (= 1.17.9)
+      jekyll (= 3.9.2)
+      jekyll-avatar (= 0.7.0)
+      jekyll-coffeescript (= 1.1.1)
+      jekyll-commonmark-ghpages (= 0.2.0)
+      jekyll-default-layout (= 0.1.4)
+      jekyll-feed (= 0.15.1)
+      jekyll-gist (= 1.5.0)
+      jekyll-github-metadata (= 2.13.0)
+      jekyll-include-cache (= 0.2.1)
+      jekyll-mentions (= 1.6.0)
+      jekyll-optional-front-matter (= 0.3.2)
+      jekyll-paginate (= 1.1.0)
+      jekyll-readme-index (= 0.3.0)
+      jekyll-redirect-from (= 0.16.0)
+      jekyll-relative-links (= 0.6.1)
+      jekyll-remote-theme (= 0.4.3)
+      jekyll-sass-converter (= 1.5.2)
+      jekyll-seo-tag (= 2.8.0)
+      jekyll-sitemap (= 1.4.0)
+      jekyll-swiss (= 1.0.0)
+      jekyll-theme-architect (= 0.2.0)
+      jekyll-theme-cayman (= 0.2.0)
+      jekyll-theme-dinky (= 0.2.0)
+      jekyll-theme-hacker (= 0.2.0)
+      jekyll-theme-leap-day (= 0.2.0)
+      jekyll-theme-merlot (= 0.2.0)
+      jekyll-theme-midnight (= 0.2.0)
+      jekyll-theme-minimal (= 0.2.0)
+      jekyll-theme-modernist (= 0.2.0)
+      jekyll-theme-primer (= 0.6.0)
+      jekyll-theme-slate (= 0.2.0)
+      jekyll-theme-tactile (= 0.2.0)
+      jekyll-theme-time-machine (= 0.2.0)
+      jekyll-titles-from-headings (= 0.5.3)
+      jemoji (= 0.12.0)
+      kramdown (= 2.3.2)
+      kramdown-parser-gfm (= 1.1.0)
+      liquid (= 4.0.3)
+      mercenary (~> 0.3)
+      minima (= 2.5.1)
+      nokogiri (>= 1.13.6, < 2.0)
+      rouge (= 3.26.0)
+      terminal-table (~> 1.4)
+    github-pages-health-check (1.17.9)
+      addressable (~> 2.3)
+      dnsruby (~> 1.60)
+      octokit (~> 4.0)
+      public_suffix (>= 3.0, < 5.0)
+      typhoeus (~> 1.3)
+    html-pipeline (2.14.3)
+      activesupport (>= 2)
+      nokogiri (>= 1.4)
+    http_parser.rb (0.8.0)
+    i18n (0.9.5)
+      concurrent-ruby (~> 1.0)
+    jekyll (3.9.2)
+      addressable (~> 2.4)
+      colorator (~> 1.0)
+      em-websocket (~> 0.5)
+      i18n (~> 0.7)
+      jekyll-sass-converter (~> 1.0)
+      jekyll-watch (~> 2.0)
+      kramdown (>= 1.17, < 3)
+      liquid (~> 4.0)
+      mercenary (~> 0.3.3)
+      pathutil (~> 0.9)
+      rouge (>= 1.7, < 4)
+      safe_yaml (~> 1.0)
+    jekyll-avatar (0.7.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-coffeescript (1.1.1)
+      coffee-script (~> 2.2)
+      coffee-script-source (~> 1.11.1)
+    jekyll-commonmark (1.4.0)
+      commonmarker (~> 0.22)
+    jekyll-commonmark-ghpages (0.2.0)
+      commonmarker (~> 0.23.4)
+      jekyll (~> 3.9.0)
+      jekyll-commonmark (~> 1.4.0)
+      rouge (>= 2.0, < 4.0)
+    jekyll-default-layout (0.1.4)
+      jekyll (~> 3.0)
+    jekyll-feed (0.15.1)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-gist (1.5.0)
+      octokit (~> 4.2)
+    jekyll-github-metadata (2.13.0)
+      jekyll (>= 3.4, < 5.0)
+      octokit (~> 4.0, != 4.4.0)
+    jekyll-include-cache (0.2.1)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-mentions (1.6.0)
+      html-pipeline (~> 2.3)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-optional-front-matter (0.3.2)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-paginate (1.1.0)
+    jekyll-readme-index (0.3.0)
+      jekyll (>= 3.0, < 5.0)
+    jekyll-redirect-from (0.16.0)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-relative-links (0.6.1)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-remote-theme (0.4.3)
+      addressable (~> 2.0)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-sass-converter (>= 1.0, <= 3.0.0, != 2.0.0)
+      rubyzip (>= 1.3.0, < 3.0)
+    jekyll-sass-converter (1.5.2)
+      sass (~> 3.4)
+    jekyll-seo-tag (2.8.0)
+      jekyll (>= 3.8, < 5.0)
+    jekyll-sitemap (1.4.0)
+      jekyll (>= 3.7, < 5.0)
+    jekyll-swiss (1.0.0)
+    jekyll-theme-architect (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-cayman (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-dinky (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-hacker (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-leap-day (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-merlot (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-midnight (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-minimal (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-modernist (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-primer (0.6.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-github-metadata (~> 2.9)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-slate (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-tactile (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-theme-time-machine (0.2.0)
+      jekyll (> 3.5, < 5.0)
+      jekyll-seo-tag (~> 2.0)
+    jekyll-titles-from-headings (0.5.3)
+      jekyll (>= 3.3, < 5.0)
+    jekyll-watch (2.2.1)
+      listen (~> 3.0)
+    jemoji (0.12.0)
+      gemoji (~> 3.0)
+      html-pipeline (~> 2.2)
+      jekyll (>= 3.0, < 5.0)
+    kramdown (2.3.2)
+      rexml
+    kramdown-parser-gfm (1.1.0)
+      kramdown (~> 2.0)
+    liquid (4.0.3)
+    listen (3.8.0)
+      rb-fsevent (~> 0.10, >= 0.10.3)
+      rb-inotify (~> 0.9, >= 0.9.10)
+    mercenary (0.3.6)
+    minima (2.5.1)
+      jekyll (>= 3.5, < 5.0)
+      jekyll-feed (~> 0.9)
+      jekyll-seo-tag (~> 2.1)
+    minitest (5.17.0)
+    nokogiri (1.14.0-x86_64-darwin)
+      racc (~> 1.4)
+    octokit (4.25.1)
+      faraday (>= 1, < 3)
+      sawyer (~> 0.9)
+    pathutil (0.16.2)
+      forwardable-extended (~> 2.6)
+    public_suffix (4.0.7)
+    racc (1.6.2)
+    rb-fsevent (0.11.2)
+    rb-inotify (0.10.1)
+      ffi (~> 1.0)
+    rexml (3.2.5)
+    rouge (3.26.0)
+    ruby2_keywords (0.0.5)
+    rubyzip (2.3.2)
+    safe_yaml (1.0.5)
+    sass (3.7.4)
+      sass-listen (~> 4.0.0)
+    sass-listen (4.0.0)
+      rb-fsevent (~> 0.9, >= 0.9.4)
+      rb-inotify (~> 0.9, >= 0.9.7)
+    sawyer (0.9.2)
+      addressable (>= 2.3.5)
+      faraday (>= 0.17.3, < 3)
+    simpleidn (0.2.1)
+      unf (~> 0.1.4)
+    terminal-table (1.8.0)
+      unicode-display_width (~> 1.1, >= 1.1.1)
+    thread_safe (0.3.6)
+    typhoeus (1.4.0)
+      ethon (>= 0.9.0)
+    tzinfo (1.2.10)
+      thread_safe (~> 0.1)
+    unf (0.1.4)
+      unf_ext
+    unf_ext (0.0.8.2)
+    unicode-display_width (1.8.0)
+    webrick (1.9.1)
+    zeitwerk (2.6.6)
+
+PLATFORMS
+  x86_64-darwin
+
+DEPENDENCIES
+  github-pages
+  webrick (~> 1.9)
+
+BUNDLED WITH
+   2.5.14

_extras/AMI-setup.md

@@ -215,4 +215,4 @@ When you are finished with your instance, you must terminate it to avoid unwante
 5. Select 'Yes, Terminate' to terminate the instance.
 
 # Reference
-This notes are adapted from the Data Carpentry Genomics Workshop [corresponding page](https://datacarpentry.org/genomics-workshop/AMI-setup/index.html)
+This notes are adapted from the Data Carpentry Genomics Workshop [corresponding page](https://datacarpentry.github.io/genomics-workshop/AMI-setup)

setup.md

@@ -29,14 +29,14 @@ If you are not in a Data Carpentry Workshop, the software you need is listed in
 
 | Software website | Used Version in Conda| Manual | Available for | Description |
 | -------- | ------------ | ------ | ------------- | ----------- |
-| [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | [0.11.9](https://anaconda.org/bioconda/fastqc) | [Help](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/)| Linux, macOS, Windows | Quality control tool for high throughput sequence data.|
-| [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic) | [0.39](https://anaconda.org/bioconda/trimmomatic) | [GitHub](https://github.com/usadellab/Trimmomatic) | Linux, macOS, Windows | A flexible read trimming tool for Illumina NGS data. |
-|[Kraken](http://ccb.jhu.edu/software/kraken2/)| [2.1.2](https://anaconda.org/bioconda/kraken2)|[GitHub](https://github.com/DerrickWood/kraken2/wiki/Manual)|Linux, macOS|A tool for taxonomic assignation for reads from metagenomics|
-|[KronaTools](https://github.com/marbl/Krona/tree/master/KronaTools) |[2.8.1](https://anaconda.org/bioconda/krona)|[GitHub](https://github.com/marbl/Krona/wiki/KronaTools)|Linux, macOS, Windows|A tool for taxonomic visualization in hierarchical pie graphs.|
-|[MaxBin2](https://sourceforge.net/projects/maxbin2/)|[2.2.7](https://anaconda.org/bioconda/maxbin2)| [SourceForge](https://sourceforge.net/projects/maxbin2/)|Linux, macOS| Tool for MAGs reconstruction|
-|[Spades](https://cab.spbu.ru/software/spades/)|[3.15.2](https://anaconda.org/bioconda/spades)|[GitHub](https://github.com/ablab/spades#sec3)|Linux, macOS| Tool for assemblies|
-|[Kraken-biom](https://github.com/smdabdoub/kraken-biom)|[1.2.0](https://anaconda.org/bioconda/kraken-biom)|[GitHub](https://github.com/smdabdoub/kraken-biom)|Linux, macOS, Windows|Tool to convert kraken reports in R readable files|
-|[CheckM-genome](https://ecogenomics.github.io/CheckM/)|[1.2.1](https://anaconda.org/bioconda/checkm-genome)|[Wiki](https://github.com/Ecogenomics/CheckM/wiki/Quick-Start#typical-workflow)|Linux, macOs, Windows|Tool to check completeness and contamination in MAGs |  
+| [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) | [0.12.1](https://anaconda.org/bioconda/fastqc) | [Help](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/)| Linux, macOS, Windows | Quality control tool for high throughput sequence data.|
+| [Trimmomatic](http://www.usadellab.org/cms/?page=trimmomatic) | [0.40](https://anaconda.org/bioconda/trimmomatic) | [GitHub](https://github.com/usadellab/Trimmomatic) | Linux, macOS, Windows | A flexible read trimming tool for Illumina NGS data. |
+| [Kraken](http://ccb.jhu.edu/software/kraken2/)| [2.1.6](https://anaconda.org/bioconda/kraken2)|[GitHub](https://github.com/DerrickWood/kraken2/wiki/Manual)|Linux, macOS|A tool for taxonomic assignation for reads from metagenomics|
+| [KronaTools](https://github.com/marbl/Krona/tree/master/KronaTools) |[2.8.1](https://anaconda.org/bioconda/krona)|[GitHub](https://github.com/marbl/Krona/wiki/KronaTools)|Linux, macOS, Windows|A tool for taxonomic visualization in hierarchical pie graphs.|
+| [MaxBin2](https://sourceforge.net/projects/maxbin2/)|[2.2.7](https://anaconda.org/bioconda/maxbin2)| [SourceForge](https://sourceforge.net/projects/maxbin2/)|Linux, macOS| Tool for MAGs reconstruction|
+| [Spades](https://cab.spbu.ru/software/spades/)|[4.2.0](https://anaconda.org/bioconda/spades)|[GitHub](https://github.com/ablab/spades#sec3)|Linux, macOS| Tool for assemblies|
+| [Kraken-biom](https://github.com/smdabdoub/kraken-biom)|[1.2.0](https://anaconda.org/bioconda/kraken-biom)|[GitHub](https://github.com/smdabdoub/kraken-biom)|Linux, macOS, Windows|Tool to convert kraken reports in R readable files|
+| [CheckM-genome](https://ecogenomics.github.io/CheckM/)|[1.2.4](https://anaconda.org/bioconda/checkm-genome)|[Wiki](https://github.com/Ecogenomics/CheckM/wiki/Quick-Start#typical-workflow)|Linux, macOs, Windows|Tool to check completeness and contamination in MAGs |  
 
 ### Option A: Using the lessons with Amazon Web Services (AWS)
 
@@ -140,19 +140,19 @@ Once your Miniconda3 is ready, follow these instructions to install and activate
 
 > ## Linux: Option 1 (recommended)
 > The easier way to install the environment is using the [specifications file](https://github.com/carpentries-lab/metagenomics-analysis/blob/gh-pages/files/spec-file-Ubuntu22.txt) 
-> for Linux Ubuntu 22.04, which has the exact versions of each tool in this environment. You can use the spec file as follows:  
+> for Linux Ubuntu 24.04, which has the exact versions of each tool in this environment. You can use the spec file as follows:  
 > ~~~
-> $ conda create --name metagenomics --file spec-file-Ubuntu22.txt
+> $ conda create --name metagenomics --file spec-file-Ubuntu24.txt
 > ~~~
 > {: .bash}
 > More information about how to use environments and spec files is available at [conda documentation](https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html)
 {: .solution}
 
 > ## Linux: option 2
 > Another way to create an environment is with a `ỳml` file.
-> This environment can be modified by adding or deleting tools in a file `metagenomics-Ubuntu22.yml`.
+> This environment can be modified by adding or deleting tools in a file `metagenomics-Ubuntu24.yml`.
 > 
-> In Ubuntu 22.04, copy this file [metagenomics-Ubuntu22.yml](https://github.com/carpentries-lab/metagenomics-analysis/blob/gh-pages/files/metagenomics-Ubuntu22.yml) 
+> In Ubuntu 24.04, copy this file [metagenomics-Ubuntu24.yml](https://github.com/carpentries-lab/metagenomics-analysis/blob/gh-pages/files/metagenomics-Ubuntu24.yml) 
 > to your computer and follow the instructions in the [video tutorial](https://youtu.be/0Ks1k9gg3E0)
 {: .solution}