Fwd: Prokka Debian package?

Looks like my CC's to the mailing list didn't make it before.

---------- Forwarded message ---------
From: Michael R. Crusoe <mcrusoe@msu.edu>
Date: Fri, Feb 20, 2015 at 7:36 PM
Subject: Re: Prokka Debian package?
To: Torsten Seemann <torsten.seemann@monash.edu>
Cc: Debian Med Project List <debian-med@lists.debian.org>

[looping in the Debian Med team]

On Fri Feb 13 2015 at 10:46:27 PM Torsten Seemann <torsten.seemann@monash.edu> wrote:

I have to list the copyright & license for each file. Here is what I figured out so far:

Files: db/hmm/HAMAP.hmm
Copyright: the UniProt Consortium
License: CC-BY-ND

My understanding is that the CC-BY-ND licence would prevent Debian from legally redistributing this file.

However I can still ship the original files plus your prokka-hamap_to_hmm script and regenerate it at install time.

Alas the package will not be allowed in Debian main but is allowed in 'non-free' (or I could split it into a data package in non-free and your scripts in 'contrib')

Files: db/hmm/Pfam.hmm
Copyright: © 1996-2011 The Pfam consortium
License: CC0

# Rfam
Files: db/cm/*
Copyright: Wellcome Trust Sanger Institute
License: CC0

Files: bin/*
Copyright: Copyright (C) 2012- Torsten Seemann
License: GPL-3

That leaves the following files unaccounted for (excluding the binaries directory which I am leaving out):

./db/genus/Enterococcus
./db/genus/Staphylococcus

These are no longer part of Prokka, the whole genus/ subfolder is gone now.

mcrusoe@athyra:~/src/prokka$ wget http://www.vicbioinformatics.com/prokka-1.11.tar.gz

mcrusoe@athyra:~/src/prokka$ tar tzf prokka-1.11.tar.gz | grep genus

prokka-1.11/db/genus/

prokka-1.11/db/genus/Enterococcus

prokka-1.11/db/genus/Staphylococcus

./db/kingdom/Archaea/sprot
./db/kingdom/Bacteria/sprot
./db/kingdom/Mitochondria/sprot
./db/kingdom/Viruses/sprot

These 3 are derived from UniProt.

Same CC-BY-ND license problem here

I see that the prokka-build_kingdom_dbs script will generate {Archaea,Bacteria,Viruses}/sprot

What about Mitochondria/sprot?

./db/hmm/CLUSTERS.hmm

http://www.ncbi.nlm.nih.gov/proteinclusters
NCBI has now abandoned it.
I took the clusters, made MSAs, then made HMMs from those!

Yay for public domain!

ALSO

In terms of APT dependencies for Debian:

libxml-simple-perl
bioperl
ncbi-blast+
hmmer (3.1) The standard 'hmmer' package is only 3.0 but 3.1 is in Debian-med i think

3.1b1-3 in Debian unstable, yep

And many others.......... Docker image might be easier!

Naw, I can handle the dependencies easily :-)

Torst

--
--Dr Torsten Seemann
--Victorian Bioinformatics Consortium, Monash University, AUSTRALIA
--Life Sciences Computation Centre, VLSCI, Parkville, AUSTRALIA
--http://www.bioinformatics.net.au/