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[BryanAbuchery]

Please help as I am stuck in trying to run TreeTuner on Mac. Here are the steps of what I have done:

(base) bryanabuchery@Abuchery ~ % brew install ruby.3.1.6
Warning: No available formula with the name "ruby.3.1.6". Did you mean [email protected]?
==> Searching for similarly named formulae and casks...
==> Formulae
[email protected]

To install [email protected], run:
brew install [email protected]
(base) bryanabuchery@Abuchery ~ % brew install [email protected]
==> Downloading https://ghcr.io/v2/homebrew/core/ruby/3.1/manifests/3.1.6
####################################################################################################################################################### 100.0%
==> Fetching [email protected]
==> Downloading https://ghcr.io/v2/homebrew/core/ruby/3.1/blobs/sha256:7c5a047c339ba80d2a14b34ef244ed9e0af7102d340b8e5f91eca4d7a0a853bf
####################################################################################################################################################### 100.0%
==> Pouring [email protected]_sonoma.bottle.tar.gz
==> Caveats
By default, binaries installed by gem will be placed into:
/opt/homebrew/lib/ruby/gems/3.1.0/bin

You may want to add this to your PATH.

[email protected] is keg-only, which means it was not symlinked into /opt/homebrew,
because this is an alternate version of another formula.

If you need to have [email protected] first in your PATH, run:
echo 'export PATH="/opt/homebrew/opt/[email protected]/bin:$PATH"' >> ~/.zshrc

For compilers to find [email protected] you may need to set:
export LDFLAGS="-L/opt/homebrew/opt/[email protected]/lib"
export CPPFLAGS="-I/opt/homebrew/opt/[email protected]/include"

For pkg-config to find [email protected] you may need to set:
export PKG_CONFIG_PATH="/opt/homebrew/opt/[email protected]/lib/pkgconfig"
==> Summary
🍺 /opt/homebrew/Cellar/[email protected]/3.1.6: 16,253 files, 45.2MB
==> Running brew cleanup [email protected]...
Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP.
Hide these hints with HOMEBREW_NO_ENV_HINTS (see man brew).
(base) bryanabuchery@Abuchery ~ % echo 'export PATH="/opt/homebrew/opt/[email protected]/bin:$PATH"' >> ~/.zshrc
(base) bryanabuchery@Abuchery ~ % ruby treetrimmer.rb
ruby: No such file or directory -- treetrimmer.rb (LoadError)
(base) bryanabuchery@Abuchery ~ % brew install BioRuby
==> Downloading https://formulae.brew.sh/api/formula.jws.json

==> Downloading https://formulae.brew.sh/api/cask.jws.json

Warning: No available formula with the name "bioruby".
==> Searching for similarly named formulae and casks...
Error: No formulae or casks found for bioruby.
(base) bryanabuchery@Abuchery ~ % gem install bio
Fetching bio-2.0.5.gem
ERROR: While executing gem ... (Gem::FilePermissionError)
You don't have write permissions for the /Library/Ruby/Gems/2.6.0 directory.
(base) bryanabuchery@Abuchery ~ % ruby -v
ruby 2.6.10p210 (2022-04-12 revision 67958) [universal.arm64e-darwin23]
(base) bryanabuchery@Abuchery ~ % source ~/.zshrc
(base) bryanabuchery@Abuchery ~ % ruby -v
ruby 3.1.6p260 (2024-05-29 revision a777087be6) [arm64-darwin23]
(base) bryanabuchery@Abuchery ~ % gem install bio
Fetching bio-2.0.5.gem
Successfully installed bio-2.0.5
Parsing documentation for bio-2.0.5
Installing ri documentation for bio-2.0.5
Done installing documentation for bio after 2 seconds
1 gem installed

A new release of RubyGems is available: 3.5.11 → 3.5.12!
Run gem update --system 3.5.12 to update your installation.

(base) bryanabuchery@Abuchery ~ % gem update --system 3.5.12
Fetching rubygems-update-3.5.12.gem
Successfully installed rubygems-update-3.5.12
Parsing documentation for rubygems-update-3.5.12
Installing ri documentation for rubygems-update-3.5.12
Done installing documentation for rubygems-update after 0 seconds
Parsing documentation for rubygems-update-3.5.12
Done installing documentation for rubygems-update after 0 seconds
Installing RubyGems 3.5.12
Successfully built RubyGem
Name: bundler
Version: 2.5.12
File: bundler-2.5.12.gem
Bundler 2.5.12 installed
RubyGems 3.5.12 installed
Regenerating binstubs
Regenerating plugins
Parsing documentation for rubygems-3.5.12
Installing ri documentation for rubygems-3.5.12

3.5.12 / 2024-06-13

Enhancements:

• Installs bundler 2.5.12 as a default gem.

Bug fixes:

• Fix gem uninstall unresolved specifications warning. Pull request
  #7667 by
  deivid-rodriguez
• Fix gem pristine sometimes failing to pristine user installed gems.
  Pull request #7664 by
  deivid-rodriguez

---

RubyGems installed the following executables:
/opt/homebrew/Cellar/[email protected]/3.1.6/bin/gem
/opt/homebrew/Cellar/[email protected]/3.1.6/bin/bundle
/opt/homebrew/Cellar/[email protected]/3.1.6/bin/bundler

Ruby Interactive (ri) documentation was installed. ri is kind of like man
pages for Ruby libraries. You may access it like this:
ri Classname
ri Classname.class_method
ri Classname#instance_method
If you do not wish to install this documentation in the future, use the
--no-document flag, or set it as the default in your ~/.gemrc file. See
'gem help env' for details.

RubyGems system software updated
(base) bryanabuchery@Abuchery ~ % ruby treetrimmer.rb
ruby: No such file or directory -- treetrimmer.rb (LoadError)
(base) bryanabuchery@Abuchery ~ % cd Documents/Masters_Genetics/Supporting_Project/Phylogeny_analyses_tests/test23
(base) bryanabuchery@Abuchery test23 % ls
Colour_Palette.xlsx Mapping_File.csv ip6k_blast.fasta
IP6K Mapping_File.xlsx ip6k_parameter_input.in.txt
IP6K.fasta Mapping_File1.csv ip6k_taxonomic_info_clean.txt
IP6K.pdf Mapping_File1.xlsx trim_IP6K_Aligned.fasta
IP6K_Aligned.fasta Tree_Ranges.csv trim_IP6K_Aligned.fasta.raxml.support
IP6K_Folder Tree_Ranges.txt trimmed_IP6K_Aligned.fasta
IP6K_Seq.xlsx Tree_Ranges.xlsx ~$Mapping_File1.xlsx
IP6K_aminoacids.txt WhatsApp
(base) bryanabuchery@Abuchery test23 % ruby treetrimmer.rb trim_IP6K_Aligned.fasta.raxml.support ip6k_parameter_input.in.txt ip6k_taxonomic_info_clean.txt > ip6k_treetrimmer.out
ruby: No such file or directory -- treetrimmer.rb (LoadError)
(base) bryanabuchery@Abuchery test23 % source ~/.zshrc
(base) bryanabuchery@Abuchery test23 % ruby treetrimmer.rb trim_IP6K_Aligned.fasta.raxml.support ip6k_parameter_input.in.txt ip6k_taxonomic_info_clean.txt > ip6k_treetrimmer.out
ruby: No such file or directory -- treetrimmer.rb (LoadError)
(base) bryanabuchery@Abuchery test23 % gem install rubygems-update
Successfully installed rubygems-update-3.5.12
Parsing documentation for rubygems-update-3.5.12
Done installing documentation for rubygems-update after 0 seconds
1 gem installed
(base) bryanabuchery@Abuchery test23 % update_rubygems
Successfully built RubyGem
Name: bundler
Version: 2.5.12
File: bundler-2.5.12.gem
Bundler 2.5.12 installed
RubyGems 3.5.12 installed
Regenerating binstubs
Regenerating plugins
Parsing documentation for rubygems-3.5.12
Installing ri documentation for rubygems-3.5.12

---

RubyGems installed the following executables:
/opt/homebrew/Cellar/[email protected]/3.1.6/bin/gem
/opt/homebrew/Cellar/[email protected]/3.1.6/bin/bundle
/opt/homebrew/Cellar/[email protected]/3.1.6/bin/bundler

Ruby Interactive (ri) documentation was installed. ri is kind of like man
pages for Ruby libraries. You may access it like this:
ri Classname
ri Classname.class_method
ri Classname#instance_method
If you do not wish to install this documentation in the future, use the
--no-document flag, or set it as the default in your ~/.gemrc file. See
'gem help env' for details.

(base) bryanabuchery@Abuchery test23 % ruby treetrimmer.rb trim_IP6K_Aligned.fasta.raxml.support ip6k_parameter_input.in.txt ip6k_taxonomic_info_clean.txt > ip6k_treetrimmer.out
ruby: No such file or directory -- treetrimmer.rb (LoadError)

I keep getting the same error: ruby: No such file or directory -- treetrimmer.rb (LoadError)

[zx0223winner]

Hi note this tree trimmer tools was developed earlier in 2013, might not be compatible with latest ruby version. Please follow the following guidelines from the link https://github.com/zx0223winner/TreeTuner/tree/main/Tutorial/TreeTuner_file_examples/Step11-14_coarse_tuning

To run this script you will need a working installation of Ruby (www.ruby-lang.org; tested with v2.5.1) and BioRuby (www.bioruby.org; tested with v2.0.3).

Type " ruby treetrimmer.rb " to see the usage. A typical command might look like: " ruby treetrimmer.rb [Newick_tree_file] [Parameter_input_file] [Taxonomic_information_file (option)] > output_file".

treetrimmer.rb can be found here https://github.com/zx0223winner/TreeTuner/blob/main/Tutorial/TreeTuner_file_examples/Step11-14_coarse_tuning/treetrimmer.rb