Monday, December 2, 2013

Rphylip in Mac OS X

I just tried Rphylip in R on Mac OS X. It appears to work fine, although the internal function findPath will not - so the full path to the PHYLIP executables needs to be supplied by the user. However I also discovered that is is very important that the installation protocol for Mac OS X described here on the PHYLIP installation page needs to be followed or else it will not work. Since this protocol involves commands that can be executed from the terminal, I may write a simple R script for Rphylip that will run these commands for the user to make it even easier.

More soon.

6 comments:

  1. Hi Liam,

    This is a very cool project you're building. A very common package manager being used by a lot of mac users is called Homebrew, which can also be used for installation of phylip (there is a "tap" of Homebrew called homebrew/science). Homebrew installs packages in it's own directory, by default "/usr/local/Cellar", and in the case of phylip, the full path is "/usr/local/Cellar/phylip/3.695/bin". Not sure if it's a worthwhile modification to the findPath function but Homebrew makes maintenance of a lot of packages quite easy.

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    1. Hi. I'm adding this now.

      Can you verify that the path is /usr/local/Cellar/phylip/3.695/bin and not /usr/local/Cellar/phylip-3.695/bin (or, for that matter, /usr/local/Cellar/phylip-3.695/exe)? I don't have a Mac (or Homebrew), but on my lab Mac PHYLIP is in /Applications/phylip-3.695/exe. Thanks!

      All the best, Liam

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    2. OK - I added this path to findPath; however I did not change setupOSX as I don't know if the 'special instructions' are required for packages managed with Homebrew. Please let me know if this would be helpful.
      All the best, Liam

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  2. the correct path is /usr/local/Cellar/phylip/3.695/bin for homebrew

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  3. The newest version of Rphylip works with the current version of phylip installed through homebrew! Thanks, Liam!

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    1. Glad to hear it! Thanks for letting me know. Liam

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