Update notebooks

bio-miga · Jun 5, 2024 · 41430a1 · 41430a1
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diff --git a/manual/part2/requirements/apt-get.md b/manual/part2/requirements/apt-get.md
@@ -13,10 +13,9 @@ Run:
 ```bash
 sudo apt-get update
 sudo apt-get install \
-  ruby ruby-sqlite3 r-base sqlite3 python3-pip pigz \
-  libcurl4-openssl-dev zlib1g zlib1g-dev \
-  ncbi-blast+ hmmer bedtools idba prodigal mcl barrnap \
-  diamond-aligner trnascan-se fastp fastani seqtk
+  ruby ruby-sqlite3 r-base sqlite3 libcurl4-openssl-dev zlib1g zlib1g-dev pigz \
+  ncbi-blast+ hmmer bedtools idba prodigal mcl barrnap diamond-aligner \
+  fastp fastani trnascan-se seqtk
 ```
 
 ## Additional Software

diff --git a/manual/part2/requirements/brew.md b/manual/part2/requirements/brew.md
@@ -2,7 +2,7 @@
 
 If you prefer to see code in action, the full installation process
 with homebrew is available as a
-[Notebook in Google Colab](https://colab.research.google.com/gist/lmrodriguezr/5b77ae113e92f2efee5060902eb78a16).
+[Notebook in Google Colab](https://colab.research.google.com/gist/lmrodriguezr/4af3b345067e862dc7903e4c78ad40ac).
 
 # Installing requirements using Homebrew
 
@@ -24,8 +24,8 @@ version using:
 
 ```bash
 brew install libyaml rbenv
-rbenv install 3.0.1
-rbenv global 3.0.1
+rbenv install 3.3.0
+rbenv global 3.3.0
 ```
 
 ## Packages

diff --git a/manual/part2/requirements/conda.md b/manual/part2/requirements/conda.md
@@ -9,7 +9,7 @@ If you don't have Conda, you can follow the
 
 If you prefer to see code in action, the full installation process
 with conda is available as a
-[Notebook in Google Colab](https://colab.research.google.com/gist/lmrodriguezr/c973df8d63c1b0d2c6ebddc39f3d92fd).
+[Notebook in Google Colab](https://colab.research.google.com/gist/lmrodriguezr/3fe4db8df4e5038ae603fde18214b148).
 
 ## Note for macOS users