Thursday, August 18, 2011


sooooo... turns out i've been fooling myself into thinking my package very easily gets and installs all the required pieces to run lociNGS. it just appeared that way because i already had everything that's needed installed on my machines. for the past couple of days i thought it was just a mac 0SX 10.5 problem, but it's actually a problem for everyone.
the problem, as i understand it, is this: numpy needs to be installed before biopython and numpy does not install with setuptools. so i've changed the script to only look for the pysam, pymongo and simplejson packages. then i'm going to have the user install Distribute, then easy_install numpy, then biopython and that should be everything. it's a little more complicated than just running the script, but doesn't require going to the internet and downloading things, only typing a couple extra lines into a terminal window. this has been driving me bonkers, so i'm moderately satisfied that i have some way to relatively easily instruct users on how to get it working at all.
these changes will appear on github and in the readme this evening (due to an unforeseen afternoon obligation). *sigh*

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