diff --git a/Gemfile b/Gemfile index 37f5eaa..db09656 100644 --- a/Gemfile +++ b/Gemfile @@ -1,2 +1,4 @@ source 'https://rubygems.org' gem 'github-pages', group: :jekyll_plugins + +gem "webrick", "~> 1.9" diff --git a/Gemfile.lock b/Gemfile.lock new file mode 100644 index 0000000..b230253 --- /dev/null +++ b/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 diff --git a/_extras/AMI-setup.md b/_extras/AMI-setup.md index f0c1b15..123e92e 100644 --- a/_extras/AMI-setup.md +++ b/_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) diff --git a/setup.md b/setup.md index e6c4f4c..047a624 100644 --- a/setup.md +++ b/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) @@ -140,9 +140,9 @@ 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) @@ -150,9 +150,9 @@ Once your Miniconda3 is ready, follow these instructions to install and activate > ## 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}