added info about setting up environment to README
corrected location of executable
changed location of Blobology outfiles to inside the Analyses folder
moved blobology commands to main make file
added remaining species to analysis
redirected useless output to /dev/null
combined separate rules for each seq using %
Moved Annotation step to main makefile

This was included in the rule for Blobology so it is only run on sequences that have
raw read data
added code to download missing JGI data

Four additional sequences have been included from JGI that weren't included in the original
analysis of single copy gene families from JGI. The downstream steps of the homolog extraction
pipeline need to be run on these sequences, but not the assembly or annotation steps. The
pipeline now obtains these sequences from JGI
changed the dependancies for the blobology and all rules

In theory, Analyses/Trees is dependent on Analyses/Alignments/Phylip/AllConcatinatedProt.phy
so I replaced the latter with the former in the all rule

Blobology is now dependent on the assemblies, which are in turn dependent on the reads, so it
shouldn't be necessary for blobology to depend directly on the reads.

The tricky part here is that "%-scaffolds.fa Reads/%_1.fastq" rule should apply whenever
the reads exist, but the JGI download rules should substitute in other cases.

I think it should be OK for the annotation step to be dependent on the Assembly step, because
the AA translations will always be downloaded from JGI right after the assemblies, so they
should always be more recent
moved annotation step to main makefile