Replace shellcmd mkdir calls with create_directory.
replace shellcmd cp with call to copy_file.
update bsmap to v2.7.4
Merge branch 'master' of ssh://git/srv/git/genome
MC16s: load sx metrics instead of setting
Skip those instrument data which should be skipped.

Currently this just means any instrument data where "ignored" is set.
SX Result: only set metrics taht are not defined
Add a move_file like copy_file.
Replace shellcmd calls with move_file and copy_file
Replace shellcmd calls with file operations in Perl.