patched miRDeep2 files can be obtained from
https://github.com/Drmirdeep/mirdeep2_patch
and the latest release from
https://github.com/rajewsky-lab/mirdeep2
A recent miRDeep2 tutorial is available here
https://drmirdeep.github.io/mirdeep2_tutorial.html
Please cite
Friedlaender M.R.; Mackowiak S.D.; Li N.; Chen W.; Rajewsky N. miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades, Nucleic Acids Research, vol. 40, pp. 37–52, Jan 2012
when using miRDeep2 in a publication.