Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Loading Errow #2

Open
BryanAbuchery opened this issue Jun 14, 2024 · 1 comment
Open

Loading Errow #2

BryanAbuchery opened this issue Jun 14, 2024 · 1 comment

Comments

@BryanAbuchery
Copy link

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
Copy link
Owner

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants