Looks like my CC's to the mailing list didn't make it before. ---------- Forwarded message --------- From: Michael R. Crusoe <[email protected]> Date: Fri, Feb 20, 2015 at 7:36 PM Subject: Re: Prokka Debian package? To: Torsten Seemann <[email protected]> Cc: Debian Med Project List <[email protected]>
[looping in the Debian Med team] On Fri Feb 13 2015 at 10:46:27 PM Torsten Seemann < [email protected]> 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/ > <http://www.bioinformatics.net.au/>* > >
