Improvements in disk_usage_for_path and reallocate

Genome::Sys->disk_usage_for_path now has better parsing and error
handling for du's output. It now has an allow_errors option that allows
it to return a number even if du emits errors (for instance, if a user
does not have read permissions for every file under the given path). To
use, simply call as so: disk_usage_for_path($path, allow_errors => 1).
Genome::Disk::Allocation->reallocate now uses this feature so it can
estimate an allocation size when du emits errors (instead of just
setting kb_requested to 0).
fixed warning about missing cnv files
Make Abyss.t clean up after itself

This test got missed in the last round of 'clean-up-after-yourself'
cleanup.
Increase mem-limit for AnnotateAndUploadVariants
ClinSeq - major refactor, convert scripts to tools, add as work flow steps, finish first complete version of DE analysis
ClinSeq fix workflow error
Switch the logging detail variable to GENOME_SYS_LOG_DETAIL.
Improvements in disk_usage_for_path and reallocate

Genome::Sys->disk_usage_for_path now has better parsing and error
handling for du's output. It now has an allow_errors option that allows
it to return a number even if du emits errors (for instance, if a user
does not have read permissions for every file under the given path). To
use, simply call as so: disk_usage_for_path($path, allow_errors => 1).
Genome::Disk::Allocation->reallocate now uses this feature so it can
estimate an allocation size when du emits errors (instead of just
setting kb_requested to 0).
fixed warning about missing cnv files
Make Abyss.t clean up after itself

This test got missed in the last round of 'clean-up-after-yourself'
cleanup.
Increase mem-limit for AnnotateAndUploadVariants
ClinSeq - major refactor, convert scripts to tools, add as work flow steps, finish first complete version of DE analysis
ClinSeq fix workflow error
Merge branch 'master' of ssh://git/srv/git/genome