Change in assembly step in response to new version of Trinity

Changes made to work with new versions of Trinity automatically. Latest
version of Trinity needs samtools to run ==> new step added to download
and install samtools.
Minor correction to running Trinity.pl

Trinity.pl was being invoked from a specific version-named directory.
Now it is invoked from the generic "trinityrnaseq-latest" directory.
Trinity dir now has version-name

Undoing a change introduced in previous commit, instead of installing
into /root/trinityrnaseq-latest/ , install into /root/trinityrnaseq-* (*
being version)
Minor correction in dir naming

Used '-' in Trinity dir name instead of '_', now corrected.
Merge pull request #8 from RamRS/trinity-update

Change in assembly step in response to new version of Trinity