add gmt bwa run-mem

A command to map fastqs to coordinate sorted bam files with bwa mem.
fix typo in help
update to look at $PIPEFAIL in bash
die when aligner_params contains -t

we used to silently remove any threading options from the aligner
params. now, we get offended at the lack of respect for the
--num-threads parameter and throw and exception.
add samtools_version param

a little weird, as this module insists on 0.1.19 (trying to use another
version will earn you an exception), but maybe nice for documentation
purposes.
perl => genome-perl as interpreter in test

do want.
remove redundant definition of pipeline commands
more detailed error reporting for failure cases
fix adding of thread params to bwa cmdline

oops, forgot () around list
update errors to use die $self->error_message
use File::Spec->catfile instead of sprintf to form paths

meow
Merge pull request #313 from tabbott/bwa-mem-tmp

add gmt bwa run-mem