add spec for bowtie 2.1.0

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
add spec for bowtie/0.12.9-1

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
bowtie 1.0.0

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>
update the doc

Signed-off-by: Sébastien Boisvert <sebastien.boisvert.3@ulaval.ca>