Update Feb. 28, 2019

Spades is a bit tricky to install. 

How it runs
---------------
spades.py is the key script that runs everything else. It in turn calls
spades_init.py, which figures out where all files are. First, it resolves
the chain of symbolic links (if any) to find out where spades.py REALLY is.
That is taken as the true path to all the rest of spades.


How it's installed on BIRCH
--------------------

To facilitate a consistent multiplatform install, we do the following:

1. In the master SPAdes directory, create a subdirectory for each
platform eg. linux-x86_64.  Also, move the share directory to the SPAdes
directory, since that is used for all platforms.

2. In each platform directory, we have a bin directory, as well as a symbolic
link to share in the parent directory.

3. in each $BIRCH/bin-$BIRCH_PLATFORM directory, create symbolic
links to the python scripts in the corresponding SPAdes subdirectory.

makelinks.sh ../pkg/spades/linux-x86_64/bin *.py
makelinks.sh ../pkg/spades/osx-x86_64/bin \*.py

4. In each SPAdes/platform/bin directory:
    - move the binaries to the $BIRCH/bin-$BIRCH_PLATFORM directory

mv spades-*  ../../../../bin-osx-x86_64

    - make symbolic links to those executables.
  
makelinks.sh ../../../../bin-linux-x86_64 spades-*

cds-mapping-stats
cds-subgraphs
mag-improve  
spades-bwa
spades-convert-bin-to-fasta
spades-core
spades-corrector-core
spades-gbuilder
spades-gmapper
spades-gsimplifier
spades-hammer
spades-ionhammer
spades-kmer-estimating
spades-kmercount
spades-read-filter
spades-truseq-scfcorrection

5. In *.py scripts, make sure the 1st line specifies python3