My attempts at In Silico Digestion

  1. Installed NumPy
    • Issue setting PYTHONPATH permanently for IDLE. Changed.bash_profile and restarted computer, but still only works in terminal.
  2. Attempted to install MySQLdb…
  3. Set up Enthought Canopy (BioPython not supported for free)
  4. Tried to Install Biopython http://biopython.org/DIST/docs/install/Installation.pdf
    • Some issue with Xcode update won’t let me (https://www.biostars.org/p/99125/)
    • building ‘Bio.cpairwise2’ extension
      Compiling with an SDK that doesn’t seem to exist: /Developer/SDKs/MacOSX10.6.sdk
      Please check your Xcode installation
      gcc -DNDEBUG -g -O3 -arch x86_64 -isysroot /Developer/SDKs/MacOSX10.6.sdk Qunused-arguments -Qunused-arguments -Qunused-arguments -I/Applications/Canopy.app/appdata/canopy-1.4.1.1975.macosx-x86_64/Canopy.app/Contents/include/python2.7 -c Bio/cpairwise2module.c -o build/temp.macosx-10.6-x86_64-2.7/Bio/cpairwise2module.o
      clang: error: no such file or directory: ‘Qunused-arguments’
      clang: warning: no such sysroot directory: ‘/Developer/SDKs/MacOSX10.6.sdk’
      error: command ‘gcc’ failed with exit status 1
  5. Ended up getting an Ubuntu virtual hardrive and getting Biopython on there
Retry (11/5/14)
Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s