Added two missing links to tools.

doc/source/installation.rst

@@ -15,6 +15,8 @@ Dependencies for running workflows
 * `SPP <https://github.com/hms-dbmi/spp>`_
 * `peakranger <http://ranger.sourceforge.net/manual1.18.html>`_
 * `MUSIC <https://github.com/gersteinlab/MUSIC>`_
+* `PePr <https://github.com/shawnzhangyx/PePr>`_
+* `hiddenDomains <http://hiddendomains.sourceforge.net/>`_
 * `samtools <https://github.com/gersteinlab/MUSIC>`_
 * `bamtools <https://github.com/pezmaster31/bamtools>`_
 * `picard <https://github.com/pezmaster31/bamtools>`_