tophat: Fails to build with clang

segment_juncs.cpp:50:17: error: expected namespace name
using namespace __gnu_cxx;

Closes #443
root 5.34.11

ROOT: Update to 5.34.11 and add HEAD for 10.9 support

This commit bumps ROOT to version 5.34.11.

It also adds a HEAD URL/branch for additional patches to the current
ROOT release.  The HEAD branch points to the *official* ROOT GitHub
mirror instead of the CERN git server simply because the CERN git server
is primarily for internal use.  While HEAD support is not strictly
necessary for 10.9, adding HEAD will allow users access to more 10.9
patches (since support is still incomplete) before the next ROOT
release.

Closes #421
edena 3.131028
ABySS-Explorer 1.3.4: New formula

ABySS-Explorer is an interactive Java application that employs a novel
graph-based representation to display a sequence assembly and
associated meta data. The tool was designed with the ABySS sequence
assembler in mind and was motivated by the need to examine assembly
structure, in particular contig connectivity and supporting paired-end
read relationships.
htqc 0.90.2: New formula

A toolkit including statistics tool for illumina high-throughput
sequencing data, and filtration tools for sequence quality, length,
tail quality, etc..