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Adding SparseMat to MacQIIME 1.6.0

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:
cd ~/Downloads/
tar -xvf AddSparseMat2MacQIIME1.6.0_OS10.6+.tgz
cd AddSparseMat2MacQIIME1.6.0_OS10.6+
./AddSparseMat.s

The install script will probably ask you for your administrative (sudo) password.

3. Check to make sure you're using SparseMat by default:
macqiime
print_biom_python_config.py

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:

System information
==================
          Platform: darwin
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

Dependency versions
===================
              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!
ċ
AddSparseMat2MacQIIME1.6.0_OS10.6+.tgz
(121k)
Jeff Werner,
Jan 31, 2013, 12:06 PM
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