syntax error

[adalgarno]

I've had trouble running both aai.rb and aai-matrix.bash and continually receive the following error for both:

enveomics/Scripts/aai.rb:23: syntax error, unexpected tSYMBEG, expecting kDO or '{' or '(' o = {bits:0, id:20, len:0, hits:50, q:fa... ^

Any recommendations on how to fix this? Thanks

[lmrodriguezr]

What version of Ruby are you using? This error looks like no support for 1.9+ key style.

[adalgarno]

I am using Ruby 2.3.1.

On Tue, Nov 29, 2016 at 11:41 AM, Luis M Rodriguez-R < notifications@github.com> wrote:

What version of Ruby are you using? This error looks like no support for 1.9+ key style.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lmrodriguezr/enveomics/issues/20#issuecomment-263642318, or mute the thread https://github.com/notifications/unsubscribe-auth/AXIL87oomG5AIJRvLEyueOeFyyCpVPAjks5rDGO6gaJpZM4K_F37 .

[lmrodriguezr]

It might be a problem with some lingering old ruby in the environment. Please send the output of the following commands:

which ruby
ruby --version
ruby enveomics/Scripts/aai.rb
./enveomics/Scripts/aai.rb

[adalgarno]

Here is the output you requested:

[dalgarno@e070 dir_2071749]$ which ruby

/usr/bin/ruby

[dalgarno@e070 dir_2071749]$ ruby --version

ruby 1.8.7 (2013-06-27 patchlevel 374) [x86_64-linux]

[dalgarno@e070 dir_2071749]$ ruby enveomics/Scripts/aai.rb

enveomics/Scripts/aai.rb:23: syntax error, unexpected tSYMBEG, expecting kDO or '{' or '('

o = {bits:0, id:20, len:0, hits:50, q:fa...

      ^

[dalgarno@e070 dir_2071749]$ ./enveomics/Scripts/aai.rb

./enveomics/Scripts/aai.rb:23: syntax error, unexpected tSYMBEG, expecting kDO or '{' or '('

o = {bits:0, id:20, len:0, hits:50, q:fa...

      ^

This is output from an interactive session on a submit node linked to HTCondor (high-throughput computing). The Ruby I thought we installed was ruby-2.3.1, as this was the version we untar-ed. Any insight you can offer on fixing this would be greatly appreciated as I have limited experience with Ruby and the HTCondor system we have been using. Thanks

On Tue, Nov 29, 2016 at 9:06 PM, Luis M Rodriguez-R < notifications@github.com> wrote:

It might be a problem with some lingering all ruby in the environment. Please send the output of the following commands:

which ruby ruby --version ruby enveomics/Scripts/aai.rb ./enveomics/Scripts/aai.rb

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/lmrodriguezr/enveomics/issues/20#issuecomment-263770325, or mute the thread https://github.com/notifications/unsubscribe-auth/AXIL8_MolmatZ6pmB3TLlQNXpq63qzvpks5rDOgugaJpZM4K_F37 .

[lmrodriguezr]

Hello @adalgarno It looks like you'll need to contact your system administrator to install a more recent version of Ruby. Unfortunately, the enveomics scripts don't offer support for Ruby pre-1.9. Alternatively, if you have a local version of a recent Ruby, you can add it to the PATH in front of /usr/bin.