[med-svn] [card-rgi] 03/03: Add mail conversation about non-free license

Fri Nov 10 14:58:59 UTC 2017

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commit bbc1637658fbbde3be8de2386251c30e9c714e77
Author: Andreas Tille <tille at debian.org>
Date:   Fri Nov 10 15:58:37 2017 +0100

    Add mail conversation about non-free license
---
 debian/copyright | 199 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 199 insertions(+)

diff --git a/debian/copyright b/debian/copyright
index 6d67c21..2cb50e2 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -12,3 +12,202 @@ License: non-free
 Files: debian/*
 Copyright: 2017 Andreas Tille <tille at debian.org>
 License: <license>
+
+
+Date: Thu, 26 Oct 2017 16:24:11 +0000
+From: "Wilson, Leigh" <wilsle at mcmaster.ca>
+To: "McArthur, Andrew" <mcarthua at mcmaster.ca>, Andreas Tille <andreas at an3as.eu>
+CC: "Raphenya, Amogelang" <raphenar at mcmaster.ca>, "milo, dsk" <milodsk at mcmaster.ca>
+Subject: RE: Please consider a free license for CARD RGI
+
+Dear Andreas-
+
+Your recent follow-up on this matter was forwarded to me.  I apologize
+if we were not clear on this earlier- as Andrew described in the email
+below we must continue to enforce licenses for commercial users in order
+to maintain the quality of CARD, I believe this makes it difficult to
+support Debian.  I hope you understand our position,
+
+Sincerely,
+
+Leigh
+
+From: McArthur, Andrew
+Sent: Friday, May 12, 2017 11:44 AM
+To: Andreas Tille
+Cc: Raphenya, Amogelang; Wilson, Leigh; milo, dsk
+Subject: Re: Please consider a free license for CARD RGI
+
+Hello Andreas,
+
+Apologies for my delayed response. As promised, we released RGI 3.2.0
+last week and this new version no longer uses MetaGeneMark, but instead
+relies on the open source Prodigal tool for gene prediction. Hopefully
+that will resolve this first license issue for Debian.
+
+In regards to the license for CARD & RGI itself, unfortunately like many
+biological databases CARD finds it hard to fund biocuration using
+traditional grant mechanisms and instead has many industrial partners
+and licensees. We cannot entertain free or open licenses. While we could
+adjust the “as is” restriction to allow path and other modifications for
+installation purposes, CARD/RGI would remain in conflict with Debian Med
+due to limits on commercial use, so I’m afraid we are unable to support
+Debian Med.
+
+We do offer power users support via Conda as our license works within
+that model and Debian Med users could secondarily install CARD RGI on
+their machines after satisfying license requirements.
+
+Sorry we cannot help more.
+
+Andrew
+
+------
+Andrew G. McArthur, Ph.D.
+Associate Professor & Cisco Research Chair in Bioinformatics
+M.G. DeGroote Institute for Infectious Disease Research,
+Department of Biochemistry and Biomedical Sciences,
+McMaster University, Hamilton, Ontario L8S 4K1, Canada
+
+office. MDCL 2322 | lab. MDCL 2317
+w. mcarthurbioinformatics.ca<http://mcarthurbioinformatics.ca> | e. mcarthua at mcmaster.ca<mailto:mcarthua at mcmaster.ca>
+p. (905) 525-9140 ext. 21663 | skype. agmcarthur
+
+
+[cid:image001.png at 01D34E55.53CF2F30]
+
+On May 12, 2017, at 8:43 AM, Andreas Tille <andreas at an3as.eu<mailto:andreas at an3as.eu>> wrote:
+
+Hi,
+
+I'm writing you on behalf of the Debian Med team which is a group inside
+Debian with the objective to package free software in life sciences and
+medicine for main Debian.  I've got a user request to package CARD RGI[1]
+
+Unfortunately the licensing conditions[2] are to restrictive to be
+considered free software.  On one hand it conflicts for instance with
+item 5 and 6 of the Debian Free Software Guidelines since it
+discrimitates users intending commercial usage.  Even worse the code
+is not even distributable inside the Debian non-free repository since
+
+  The Materials not be modified and used "as is"
+
+means we can not even apply some patches that would be really needed to
+do some sensible distribution to install the code globally on a machine
+for every user (as you even suggest in your installation instruction
+_docs/README, paragraph Commands for Running RGI system-wide) since this
+would mean changing some pathes inside the code.  For instance when
+starting my unfinished packaging attemt I had created some patches[4]
+that are permitted by the above sentence.
+
+It would be great if you might consider some well known free license as
+for instance is used by the several tools (prodigal, ncbi-blast+ and
+python-biopython) you are basing your code upon.  According the
+experiences we gathered in the Debian Med team the restrictive license
+you are using is not really helping to increase the acceptance of the
+code inside the scientific community nor does it encourage others to
+provide contributions that would enhance your code.
+
+Kind regards and thanks for considering
+
+      Andreas.
+
+
+[1] https://card.mcmaster.ca/
+[2] https://card.mcmaster.ca/about
+[3] https://www.debian.org/social_contract#guidelines
+[4] https://anonscm.debian.org/git/debian-med/card-rgi.git/tree/debian/patches
+
+--
+http://fam-tille.de
+
+
+On Apr 29, 2017, at 4:14 PM, McArthur, Andrew <mcarthua at mcmaster.ca<mailto:mcarthua at mcmaster.ca>> wrote:
+
+Hello Andrea,
+
+Much thanks for your email. Your timing is good, we’ve been working on this issue and are about to roll out a new version of RGI that use Prodigal instead.
+
+In addition, we are adjusting the older version downloads to not include the MetaGeneMark binary.
+
+I’ll send you a second email once RGI 3.2.0 based on Prodigal is available.
+
+All the best,
+Andrew McArthur
+
+------
+Andrew G. McArthur, Ph.D.
+Associate Professor & Cisco Research Chair in Bioinformatics
+M.G. DeGroote Institute for Infectious Disease Research,
+Department of Biochemistry and Biomedical Sciences,
+McMaster University, Hamilton, Ontario L8S 4K1, Canada
+
+office. MDCL 2322 | lab. MDCL 2317
+w. mcarthurbioinformatics.ca<http://mcarthurbioinformatics.ca/> | e. mcarthua at mcmaster.ca<mailto:mcarthua at mcmaster.ca>
+p. (905) 525-9140 ext. 21663 | skype. agmcarthur
+
+
+<image002.png>
+
+On Apr 25, 2017, at 11:32 AM, Andreas Tille <tille at debian.org<mailto:tille at debian.org>> wrote:
+
+Hello,
+
+I'm writing you on behalf of the Debian Med team which is a group inside
+Debian with the objective to package free software in life science and
+medicine for official Debian.  I've got a user request to package CARD
+RGI and thus I had a look into your download files.
+
+As far as I can see you are including a binary copy of MetaGeneMark
+version 3.26 inside the download archive[1].  The LICENSE file included
+says:
+
+...
+  2. Prohibited Uses.  Licensee may not:
+
+  a) transfer, distribute, lease or sub-license the Product.
+...
+
+As far as I understand you've got a licensing key for your use but you
+are distributing this together with your software which is prohibited.
+
+I confirm that as a Debian developer I'd really like if software authors
+would consider free licenses.  I took the issue above as a reason to
+write to GeneMark authors to do change their license[2].  I think it
+would be in your interest to join the petition and clarify the license
+for your specific case.
+
+In case you actually received a more permissive license from GeneMark
+developers please add some additional information to the licensing text.
+
+And BTW, if we are at it:  You might like to consider a free license
+for RGI as well. :-)
+
+Kind regards
+
+       Andreas.
+
+
+[1] https://card.mcmaster.ca/download/1/software-v3.1.1.tar.gz
+[2] https://lists.debian.org/debian-med/2017/04/msg00041.html
+
+--
+http://fam-tille.de<http://fam-tille.de/>
+
+
+------
+Andrew G. McArthur, Ph.D.
+Associate Professor & Cisco Research Chair in Bioinformatics
+M.G. DeGroote Institute for Infectious Disease Research,
+Department of Biochemistry and Biomedical Sciences,
+McMaster University, Hamilton, Ontario L8S 4K1, Canada
+
+office. MDCL 2322 | lab. MDCL 2317
+w. mcarthurbioinformatics.ca<http://mcarthurbioinformatics.ca/> | e. mcarthua at mcmaster.ca<mailto:mcarthua at mcmaster.ca>
+p. (905) 525-9140 ext. 21663 | skype. agmcarthur
+
+
+[cid:image001.png at 01D34E55.53CF2F30]
+
+
+

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