VirusSeeker: RepeatMasker missed in dependencies (Was: VirusSeeker - sorting the Downloads section)
Hi Everyone, I've been quietly chiseling the packaging of virusseeker-virome, but I missed the proper RepeatMasker dependency in the initial list; Debian provides a few packages related to that software, and I mistakenly thought it was available already. For reference, it is the software available at: http://www.repeatmasker.org/RMDownload.html Unfortunately, I understand that it is licensed under OSL 2.1, and that this license does not look DFSG compliant, nor seems compatible with the GPL: https://wiki.debian.org/DFSGLicenses#Open_Software_License_.28OSL.29_v1.1 https://www.gnu.org/licenses/license-list.html#OSL At some point, I wondered if it would be possible to get RepeatMasker into "non-free", and having VirusSeeker into "contrib" then, but I'm not sure that this is legally doable since VirusSeeker is GPL. Have you already met similar situation in the past ? If so, how has it been dealt with ? mer...@debian.org, on 2020-04-10 07:40:42 +0300: > 1. Replace hard-coded database paths with environment variables, say, > VIRUSSEEKER_NCBI_NT. Then prior to running the VirusSeeker the user > would need to download the databases and set these environment variables > to their locations. > > 2. Make their paths configurable via a configuration file (under /etc, > possibly) listing paths for the databases. After installing the Debian > package, the user would have to edit this configuration file to point to > the database locations. Hi Andrius, Thank you for your thoughts, even if I'm a bit late. Reading through the script, even using environment variables, there is a quite big share of hard-coded paths, so would probably attempt to contact upstream in any case. Kind Regards, -- Étienne Mollier Fingerprint: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d Help find cures against the Covid-19 ! Give CPU cycles: * Rosetta@home: https://boinc.bakerlab.org/rosetta/ * Folding@home: https://foldingathome.org/ signature.asc Description: PGP signature
Re: VirusSeeker: RepeatMasker missed in dependencies (Was: VirusSeeker - sorting the Downloads section)
Hi Étienne, On Thu, May 07, 2020 at 11:24:00PM +0200, Étienne Mollier wrote: > I've been quietly chiseling the packaging of virusseeker-virome, > but I missed the proper RepeatMasker dependency in the initial > list; Debian provides a few packages related to that software, > and I mistakenly thought it was available already. For > reference, it is the software available at: > > http://www.repeatmasker.org/RMDownload.html Thanks a lot for checking. > Unfortunately, I understand that it is licensed under OSL 2.1, > and that this license does not look DFSG compliant, nor seems > compatible with the GPL: > > > https://wiki.debian.org/DFSGLicenses#Open_Software_License_.28OSL.29_v1.1 > https://www.gnu.org/licenses/license-list.html#OSL > > At some point, I wondered if it would be possible to get > RepeatMasker into "non-free", and having VirusSeeker into > "contrib" then, but I'm not sure that this is legally doable > since VirusSeeker is GPL. > > Have you already met similar situation in the past ? > If so, how has it been dealt with ? Hmmm, I do not remember but non-free is ugly for several technical reasons (no autobuilders, no autopkgtests, no QA checks etc.) Thus the first thing I do is contacting upstream to consider changing their license. Would you mind doing so? If yes, I would consider mentioning our COVID-19 sprint and that a free license would support us in our fight against the pandemic. Kind regards Andreas. > mer...@debian.org, on 2020-04-10 07:40:42 +0300: > > 1. Replace hard-coded database paths with environment variables, say, > > VIRUSSEEKER_NCBI_NT. Then prior to running the VirusSeeker the user > > would need to download the databases and set these environment variables > > to their locations. > > > > 2. Make their paths configurable via a configuration file (under /etc, > > possibly) listing paths for the databases. After installing the Debian > > package, the user would have to edit this configuration file to point to > > the database locations. > > Hi Andrius, > > Thank you for your thoughts, even if I'm a bit late. Reading > through the script, even using environment variables, there is > a quite big share of hard-coded paths, so would probably attempt > to contact upstream in any case. > > Kind Regards, > -- > Étienne Mollier > Fingerprint: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d > Help find cures against the Covid-19 ! Give CPU cycles: > * Rosetta@home: https://boinc.bakerlab.org/rosetta/ > * Folding@home: https://foldingathome.org/ -- http://fam-tille.de
Re: VirusSeeker: RepeatMasker missed in dependencies (Was: VirusSeeker - sorting the Downloads section)
> On Thu, May 07, 2020 at 11:24:00PM +0200, Étienne Mollier wrote: > > > > At some point, I wondered if it would be possible to get > > RepeatMasker into "non-free", and having VirusSeeker into > > "contrib" then, but I'm not sure that this is legally doable > > since VirusSeeker is GPL. Le Thu, May 07, 2020 at 11:39:18PM +0200, Andreas Tille a écrit : > > Hmmm, I do not remember but non-free is ugly for several technical > reasons (no autobuilders, no autopkgtests, no QA checks etc.) Thus > the first thing I do is contacting upstream to consider changing > their license. Would you mind doing so? If yes, I would consider > mentioning our COVID-19 sprint and that a free license would support > us in our fight against the pandemic. Hi all, +1 in principle, but I note that RepeatMasker has TRF (Tandem Repeat Finder) in its dependencies, which is also non-free... http://tandem.bu.edu/trf/trf.license.html Have a nice day, Charles -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Akano, Uruma, Okinawa, Japan
Re: VirusSeeker: RepeatMasker missed in dependencies (Was: VirusSeeker - sorting the Downloads section)
Hi Everyone, Charles Plessy, on 2020-05-08 09:19:59 +0900: > > On Thu, May 07, 2020 at 11:24:00PM +0200, Étienne Mollier wrote: > > > > > > At some point, I wondered if it would be possible to get > > > RepeatMasker into "non-free", and having VirusSeeker into > > > "contrib" then, but I'm not sure that this is legally doable > > > since VirusSeeker is GPL. > > Le Thu, May 07, 2020 at 11:39:18PM +0200, Andreas Tille a écrit : > > > > Hmmm, I do not remember but non-free is ugly for several technical > > reasons (no autobuilders, no autopkgtests, no QA checks etc.) Thus > > the first thing I do is contacting upstream to consider changing > > their license. Would you mind doing so? If yes, I would consider > > mentioning our COVID-19 sprint and that a free license would support > > us in our fight against the pandemic. Thanks Andreas for reminding the technical implications, which /append/ to the legal ones. > +1 in principle, but I note that RepeatMasker has TRF (Tandem Repeat > Finder) in its dependencies, which is also non-free... > > http://tandem.bu.edu/trf/trf.license.html Thanks Charles for having spotted this, let's pull this wire and see where it leads. It sounds like licensecheck/scan-copyrights will be quite useful. > Have a nice day, Kind Regards, -- Étienne Mollier Fingerprint: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d Help find cures against the Covid-19 ! Give CPU cycles: * Rosetta@home: https://boinc.bakerlab.org/rosetta/ * Folding@home: https://foldingathome.org/ signature.asc Description: PGP signature
Re: VirusSeeker: RepeatMasker missed in dependencies (Was: VirusSeeker - sorting the Downloads section)
On Fri, May 08, 2020 at 09:19:59AM +0900, Charles Plessy wrote: > > their license. Would you mind doing so? If yes, I would consider > > mentioning our COVID-19 sprint and that a free license would support > > us in our fight against the pandemic. > > Hi all, > > +1 in principle, but I note that RepeatMasker has TRF (Tandem Repeat > Finder) in its dependencies, which is also non-free... > > http://tandem.bu.edu/trf/trf.license.html So please take up the TRF ball again. At least one of the authors https://lists.debian.org/debian-med/2016/06/msg00093.html I kept on pinging (feel free to browse the archive) and we should really do more work here. I repeatedly said now is the time for this and that non-programmers could do some extremely valuable contribution to join this effort. Kind regards Andreas. -- http://fam-tille.de
Re: VirusSeeker: RepeatMasker missed in dependencies (Was: VirusSeeker - sorting the Downloads section)
Hi Étienne, On 2020-05-08 00:24, Étienne Mollier wrote: > Thank you for your thoughts, even if I'm a bit late. Reading > through the script, even using environment variables, there is > a quite big share of hard-coded paths, so would probably attempt > to contact upstream in any case. Contacting the upstream is the best solution here. It would be great if they agree to switch to either environment variables or configuration files. Best, Andrius signature.asc Description: OpenPGP digital signature
Re: VirusSeeker: RepeatMasker missed in dependencies (Was: VirusSeeker - sorting the Downloads section)
Hi Andrius, mer...@debian.org, on 2020-05-13 12:02:29 +0300: > On 2020-05-08 00:24, Étienne Mollier wrote: > > Thank you for your thoughts, even if I'm a bit late. Reading > > through the script, even using environment variables, there is > > a quite big share of hard-coded paths, so would probably attempt > > to contact upstream in any case. > > Contacting the upstream is the best solution here. It would be great if > they agree to switch to either environment variables or configuration files. Definitely, I opened an issue in what looks like the current source code repository: https://github.com/guoyanzhao/VirusSeeker-Virome/issues/10 Will see how things go.. Kind Regards, -- Étienne Mollier Fingerprint: 5ab1 4edf 63bb ccff 8b54 2fa9 59da 56fe fff3 882d Help find cures against the Covid-19 ! Give CPU cycles: * Rosetta@home: https://boinc.bakerlab.org/rosetta/ * Folding@home: https://foldingathome.org/ signature.asc Description: PGP signature
Re: VirusSeeker: RepeatMasker missed in dependencies (Was: VirusSeeker - sorting the Downloads section)
Hi Étienne, On 2020-05-13 22:07, Étienne Mollier wrote: > Definitely, I opened an issue in what looks like the current > source code repository: > > https://github.com/guoyanzhao/VirusSeeker-Virome/issues/10 Looks good! Best, Andrius signature.asc Description: OpenPGP digital signature
