Re: [EMBOSS] Files included in EMBOSS but licensed under Creative Commons Attribution-NoDerivs
On 28/07/2011 15:38, Charles Plessy wrote: Dear EMBOSS developers, (CC Debian Med mailing list) while working on upgrading Debian's emboss package to version 6.4.0 (congratulations, by the way), I found some files in EMBOSS that are not considered ‘Free software’ by Debian. They were actually present in past releases as well. Here is their list: test/data/amir.swiss test/data/uniprotft.sw test/swiss/seq.dat test/swnew/trembl.dat Huh? Example entries from UniProt? We can of course remove them from the distribution but then the QA tests will not work if anyone tries them. I suspect amir.swiss predates this UniProt licensing, but the others are more recently updated. Anyway, EMBOSS will work perfectly well without them. You can just delete them. and emboss/data/dbxref.txt That one can go. It was a source for the DRCAT.dat data resource catalogue and yes we do have permission from UniProt to use it. Their license is Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0), and it disallows modification of the files. The presence of these files in EMBOSS makes it impossible for Debian to redistribute it in our operating system. I have confirmed with the UniProt consortium's helpdesk that, even in isolation, these files are covered by the CC BY-ND license. I see three possible solutions. a) Remove the files in Debian's EMBOSS package. b) Distribute EMBOSS with the files, but in the non-free section of the Debian archive. c) Replace the files by Free equivalents, for instance by re-creating records from scratch. I am not very comfortable with any of the solutions, and was wondering if you would have suggestions ? I will also have words with the UniProt folk at EBI and if it really is not possible to include a few example entries with EMBOSS then I'll check with the other Open Bio projects. This is really silly. regards, Peter Rice EMBOSS Team ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Files included in EMBOSS but licensed under Creative Commons Attribution-NoDerivs
On 28/07/2011 15:38, Charles Plessy wrote: Dear EMBOSS developers, (CC Debian Med mailing list) while working on upgrading Debian's emboss package to version 6.4.0 (congratulations, by the way), I found some files in EMBOSS that are not considered ‘Free software’ by Debian. They were actually present in past releases as well. Their license is Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0), and it disallows modification of the files. The presence of these files in EMBOSS makes it impossible for Debian to redistribute it in our operating system. I have confirmed with the UniProt consortium's helpdesk that, even in isolation, these files are covered by the CC BY-ND license. I see three possible solutions. Ummm in what sense would *you* be modifying the files? UniProt's license http://www.uniprot.org/help/license says License disclaimer License We have chosen to apply the Creative Commons Attribution-NoDerivs License to all copyrightable parts of our databases. This means that you are free to copy, distribute, display and make commercial use of these databases in all legislations, provided you give us credit. However, if you intend to distribute a modified version of one of our databases, you must ask us for permission first. So I see no problem for EMBOSS in including the files. The only problem is for someone modifying the files and redistributing them without permission ... but strictly that would not apply to most uses of a UniProt entry (otherwise you could not use one entry as input and distribute the results). The licensing is there to prevent redistribution of UniProt without permission. Anyway, you can just delete them from the Debian duistribution of EMBOSS - and find your own way to run the QA tests. I don't think we have a problem. regards, Peter Rice EMBOSS Team regards, Peter Rice ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Files included in EMBOSS but licensed under Creative Commons Attribution-NoDerivs
Charles Plessy wrote: a) Remove the files in Debian's EMBOSS package. b) Distribute EMBOSS with the files, but in the non-free section of the Debian archive. c) Replace the files by Free equivalents, for instance by re-creating records from scratch. d) Add a small script that wget's each file from its original distribution site and installs it in the right place. Have the package install script either ask if it should run this script, or have it issue a message which describes the issue and leaves it up to the user to run the script. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Files included in EMBOSS but licensed under Creative Commons Attribution-NoDerivs
I would prefer (c) or the newly-added (d) myself Cheers, Wolfgang -- Dr. Wolfgang Rumpf Senior Product Specialist Director of Support, Rescentris Inc. Adjunct Faculty, Dept. of Biotechnology, UMUC -- wolfgang.ru...@rescentris.com wolfgang.ru...@gmail.com Mobile - (614) 638-6797 Skype - wolfgang.rumpf -- Read my Blog - QuantumThoughts - at http://culture.no-ip.org/quantumthoughts -- On Jul 28, 2011, at 11:06 AM, David Mathog wrote: Charles Plessy wrote: a) Remove the files in Debian's EMBOSS package. b) Distribute EMBOSS with the files, but in the non-free section of the Debian archive. c) Replace the files by Free equivalents, for instance by re-creating records from scratch. d) Add a small script that wget's each file from its original distribution site and installs it in the right place. Have the package install script either ask if it should run this script, or have it issue a message which describes the issue and leaves it up to the user to run the script. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
Re: [EMBOSS] Files included in EMBOSS but licensed under Creative Commons Attribution-NoDerivs
I would prefer (d) and I know packages where this is realized like this. For example in SuSE the msttf fonts. Regards, Stefan 2011/7/28 Wolfgang Rumpf wolfgang.ru...@gmail.com: I would prefer (c) or the newly-added (d) myself Cheers, Wolfgang -- Dr. Wolfgang Rumpf Senior Product Specialist Director of Support, Rescentris Inc. Adjunct Faculty, Dept. of Biotechnology, UMUC -- wolfgang.ru...@rescentris.com wolfgang.ru...@gmail.com Mobile - (614) 638-6797 Skype - wolfgang.rumpf -- Read my Blog - QuantumThoughts - at http://culture.no-ip.org/quantumthoughts -- On Jul 28, 2011, at 11:06 AM, David Mathog wrote: Charles Plessy wrote: a) Remove the files in Debian's EMBOSS package. b) Distribute EMBOSS with the files, but in the non-free section of the Debian archive. c) Replace the files by Free equivalents, for instance by re-creating records from scratch. d) Add a small script that wget's each file from its original distribution site and installs it in the right place. Have the package install script either ask if it should run this script, or have it issue a message which describes the issue and leaves it up to the user to run the script. Regards, David Mathog mat...@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss ___ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
