chapmanb/bcbio-nextgen — pull request #101 by mariogiov (2013-09-10 12:19:17+00:00)
Title: Expand shell variables into paths in config_utils.py

Not sure if this is an update you'd like or not but it fixes an issue I was having where the shell variable `$SNPEFF_HOME` (which we use in a config file) was not being expanded into the actual path, resulting in a file-not-found OSError for `nosetests -a speed=1`. I note that similar variables ($GATK_HOME, $PICARD_HOME) are expanded successfully so this was probably overlooked (original call from `bcbio.variation.effects._get_snpeff_genome()`)