Add bowtie/1.1.1

bowtie/1.1.1 is an update of bowtie/1.0.1

Signed-off-by: James Oguya <oguyajames@gmail.com>
bowtie/1.1.1 fixing a typo in module definition

Signed-off-by: James Oguya <oguyajames@gmail.com>
Add bowtie2/2.2.3

bowtie2/2.2.3 is an update of bowtie2/2.2.2 with some bug fixes:
- Fixed a bug that made loading an index into memory crash sometimes.
- Fixed a silent failure to warn the user in case the -x option is missing.
- Updated al, un, al-conc and un-conc options to avoid confusion in cases
where the user does not provide a base file name.
- Fixed a spurious assert that made bowtie2-inspect debug fail.

Signed-off-by: James Oguya <oguyajames@gmail.com>
Add tophat2/2.0.13

so according to tophat2 changelog, v2.0.13 removed SAMtools as an
external dependency in order to avoid incompatibility issues with recent
and future changes of SAMtools and its code library (an older, stable
SAMtools version is now packaged with TopHat).

Signed-off-by: James Oguya <oguyajames@gmail.com>
tophat2/2.0.13 load bowtie2 dependency

tophat2 depends on bowtie to perform bowtie related tasks, and so we should
load bowtie2 module

Signed-off-by: James Oguya <oguyajames@gmail.com>
Add masurca/2.3.2

Signed-off-by: Alan Orth <alan.orth@gmail.com>