create temp dir in cwd
create temp dir in cwd
Merge branch 'bacteria_pan_genome' of github.com:andrewjpage/PathFind into bacteria_pan_genome
check user gffs created
extra bracket in pan genome script
hard link to vrtrack libs
cwd in log test
Merge pull request #20 from andrewjpage/bacteria_pan_genome

Bacteria pan genome updates
Bug fixes and feature updates
Merge pull request #21 from carlacummins/master

Bug fixes and feature updates
use reference name when looking up reference files
Merge pull request #22 from andrewjpage/reffind_ref_searching

use reference name when looking up reference files