January 31, 2013
This will work only in OS 10.6 and up. To add SparseMat capabilities to your biom-format library in MacQIIME 1.6.0, please follow these instructions. This will make some OTU matrix operations work more quickly.
1. Download this file into your ~/Downloads/ folder.
2. In the Terminal, open it up and install:
The install script will probably ask you for your administrative (sudo) password.
3. Check to make sure you're using SparseMat by default:
You will have to exit and re-initiate any open macqiime terminal subshells for the change to take effect. That second command should print the following:
Python/GCC version: 2.7.3 (default, Dec 19 2012, 09:12:08) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
Python executable: /macqiime/bin/python
NumPy version: 1.5.1
biom-format library version: 1.1.1
biom-format script version: 1.1.1
biom-format package information
SparseObj type: biom.sparsemat.SparseMat
Please let me know if you have any problems; thanks!