Cufflinks: still fails with clang 425
soapdenovo: Specify the version explicitly

The version number is incorrectly identified as `V1.05.src`.
openblas: use depends_on :fortran
petsc: use depends_on :fortran
scalapack: use depends_on :fortran
wcslib: use depends_on :fortran
lammps: use depends_on :fortran
abyss: use depends_on :mpi
lammps: use depends_on :mpi
mrbayes: use depends_on :mpi
parmetis: use depends_on :mpi
petsc: use depends_on :mpi
ray: use depends_on :mpi
scalapack: use depends_on :mpi
scotch: use depends_on :mpi
trilinos: use depends_on :mpi
tophat: Add -lboost_thread-mt to LIBS

Fix the error
```
undefined reference to `typeinfo for boost::detail::thread_data_base'
```
tophat 2.0.8b

Closes #239
cufflinks: Fix a build error

`./lemon/bits/base_extender.h:362:21: error: ‘aNode’ was not declared`
cufflinks: Fix boost link errors

```
Undefined reference to `boost::system::system_category`
and `boost::detail::set_tss_data`.
```