Update Nov. 27, 2025
Spades v4.2.0

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.
(We have to escape the * as \*)

makelinks.sh ../pkg/spades/$BIRCH_PLATFORM/bin \*.py


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

mv spades-*  ../../../../bin-$BIRCH_PLATFORM
mv binspreader path* spaligner ../../../../bin-$BIRCH_PLATFORM


    - make symbolic links to those executables.
  
makelinks.sh ../../../../bin-$BIRCH_PLATFORM spades-\*
SOURCE=../../../../bin-$BIRCH_PLATFORM
ln -s $SOURCE/binspreader
ln -s $SOURCE/pathracer
ln -s $SOURCE/pathracer-seq-fs
ln -s $SOURCE/spaligner

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