If bowtie is not on the path of the user(s) expected to run bowtie, the location of the executable may be configured as follows:
# Specify the bowtie command to use, useful if you want to use a specific bowtie version not on the path
# or would like special options. For example, to quiet bowtie output. Defaults to 'bowtie' on user $PATH
$bowtie_exe = '/my/bowtie/directory/bowtie --quiet';
Likewise, if users mostly work with only a single genome, that can be configured as the default as follows: ADD INFO ABOUT 'chrX' BUG IF NOT FIXED
# Specify the genome idnex to use, should be a full path excluding the file extension or just the name of
# the genome index if the index is in the indexes folder of the bowtie installation. Defaults to 'mm9'
#$bowtie_idx = '/path/to/bowtie/indexes/my_reference_genome_name';
