Initial commit of cleaned up BLAST_makeflow.
Parse shell-like line continuation in makeflow files
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.
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.
BWA_makeflow now creates cat_bwa and fastq_reduce internally
Actually included bwa_makeflow in this commit
Revised bwa_makeflow to remove scripts if they exist
write dax to file instead of stdout
create replica catalog for all input files
create transform catalog for dax export
example usage instructions to plan DAX version of workflow