fix typo in Cufflinks easyconfigs
add Cufflinks 2.1.1 ictce/5.5.0 easyconfig + required patch (curtosy @JensTimmerman)
add ictce/5.5.0 easyconfigs for Bowtie2, TopHat, GMap, HTSeq + dependencies
init ispc & mcpp

Signed-off-by: Fotis Georgatos <fotis.georgatos@uni.lu>
CMake: updated to 2.8.12 with GCC 4.8.2
Clang: first attempt to easyconfig for 3.4
Clang: disable optarch, this cause the build to fail
Clang: reorganized patches for clang-3.4
Clang: reorganize the patches correctly
ClangGCC: updated toolchain to clang-3.4
Added CLooG for Clang
Renamed CLooG to include toolchain
Clang: build with polly by default
Added GMP with GCC-4.8.2 for Clang
SOAPdenovo2
fix quote business

Signed-off-by: Fotis Georgatos <fotis.georgatos@uni.lu>
removed superfluous lines in patch.
fixed white space issues.
Clang-3.4: use polly
minor style fixes in SOAPdenovo2 easyconfigs