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Setting up Emacs to interact with Pathway Tools in Lisp Mode

asked 2013-05-01 13:39:34 -0500

anonymous user

Anonymous

I’d like to know how “power users” set up their Pathway Tools environment for API hacking. Can anyone help me out?

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answered 2015-06-19 19:18:39 -0500

quang777 gravatar image

Pathway Tools has a built-in Lisp environment that you can use to programmatically query and modify your Pathway / Genome Database. You can access the Lisp listener by starting up Pathway Tools like so: pathway-tools -lisp. Interacting with it via Emacs provides you with a fully-integrated IDE that provides debugging support, syntax high-lighting, and syntax-aware navigation commands. The recommended Common Lisp interaction platform for Pathway Tools users is SLIME, the Superior Lisp Interaction Mode for Emacs.

These instructions were generously provided by Jeremy Zucker.

  1. Download SLIME: slime-current.tgz
  2. Add this to your .emacs file:
    (setq slime-lisp-implementations
         '((ptools ("/usr/local/bin/pathway-tools" "-api" "-lisp") :init slime-init-command)))
    
    (add-to-list 'load-path "/path/to/slime")
  3. Now, if you try to run M-x slime, you will get an error like this:
    Condition: Can't locate the module "SCM"
  4. The current workaround for this is to download Allegro Common Lisp (ACL), and copy files.bu into the pathway-tools exe directory (shown below).
    Note, you do not need a license to download ACL. You only need one if you are planning to run ACL.
  5. This is how you would do this on a Mac:
    cp /Applications/AllegroCL/files.bu /usr/local/pathway-tools/aic-export/pathway-tools/12.5/exe
  6. Now, running M-x slime in emacs should just work.
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Asked: 2013-05-01 13:39:34 -0500

Seen: 1,261 times

Last updated: Jun 19 '15