Initial commit of cleaned up BLAST_makeflow.
automatically detect number of gpus available

Wraps nvidia-smi to query the number of gpus installed.
copy gpu_detection script when setting up worker's working directory
Parse shell-like line continuation in makeflow files
pass gpu count via stdout instead of exit codes.

Exit codes can be ambiguous.
lookup executable in search path
Added sample files, cleaned up cat_bwa.pl, and converted bwa_makeflow to take strings for inputs.
Removed extraneous files in commit.
Cleaned up files and moved to properly named directory
Removed large example files, will replace with smaller files in later commit.
Added copyright information. Removed .pl from cat_bwa.
Slight modification to the cat_bwa header comment.
prepend cwd unless test string is an absolute path
generalize to any search string.

Also includes memory usage improvements.
Use alien_cache option for cvmfs in parrot
Change malloc to string_format for cvmfs options
Honor $TMPDIR for default value of pfs_temp_dir
Add --cvmfs-alien-cache command line option.
Cleanup cvmfs locks dir.

Now that the cvmfs locks dir pathname is not the same for every parrot
run, we need to remove it at the end of execution.
Fixes for cctools_gpu_autodetect.

Renamed gpu_autodetect to cctools_gpu_autodetect.

Redirected error messages to stderr.

Fixed bashisims.