SPAdes for Debian

[Andreas Tille <andreas@an3as.eu>]

Hello,

I'm writing you on behalf of the Debian Med project which has the goal
to package Free Software which is relevant in the field of medicine and
biology for main Debian.  Here you can see a list of software we have
just included in the field of biology[1].

I now wanted to give SPAdes a try and did the packaging in SVN[2].  The
most important thing you might like to know is that I followed the
Debian philosophy to use the just packaged code and thus I skipped the
code copies of boos, python-yaml and python-joblib.  You also might like
to notice that Debian always delivers an executable under /usr/bin which
is in this case named spades and dispades consisting of a wrapper to
spades.py which finds the main spades binary under /usr/lib/spades/bin
but these are technical details.

The main paoint why I'm writing you is the fact that I was running the
suggested test

  /usr/bin/spades --pe1-1 /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz --pe1-2 /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz -o spades_test

and compared it with the binary version you are providing at your
download page to make sure the result will be the same.  I used the
attached script where I kept the result created with the prebuilded
binary in the directory spades_binary_result/.  I can confirm that
according to this test the Debian packaged version creates the same
result.

The problem I have is that I have access to some other computer on which
a copy of SPAdes 2.5 is installed (I assume from the prebuilded binary
but I can not say for sure).  When running the very same test I get
different *.fasta/*.fastq results.  What I'm wondering now:  What is the
reason for the differences in the test between version 2.5 and 3.0.  I
think it would make sense to provide some kind of test suite to ensure
users that their results have good chances to be reproducible.

Kind regards

        Andreas.

[1] http://blends.debian.org/med/tasks/bio
[2] http://anonscm.debian.org/viewvc/debian-med/trunk/packages/spades/trunk/

-- 
http://fam-tille.de

#!/bin/sh
spades --pe1-1 /usr/share/spades/test_dataset/ecoli_1K_1.fq.gz --pe1-2 /usr/share/spades/test_dataset/ecoli_1K_2.fq.gz -o spades_test
for fcmp in `find spades_binary_result -name "*.fast*" -o -name "*.data"` ; do
    testres=`echo $fcmp | sed 's/^spades_binary_result/spades_test/'`
    if ! zdiff $fcmp $testres ; then
	echo "comparison failed for file $testres"
        exit
    fi
done