https://sourceforge.net/p/tapdancebio/wiki/Bowtie%2520Configuration/Recent changes to Bowtie ConfigurationenFri, 11 Nov 2011 21:56:42 -0000https://sourceforge.net/p/tapdancebio/wiki/Bowtie%2520Configuration/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';Jesse ErdmannFri, 11 Nov 2011 21:56:42 -0000https://sourceforge.net5aae594c4def56521232428ca0da5b097363d8f1