Packaging libsis-jhdf5-java -- help needed
Hi everyone, I have been trying to package libsis-jhdf5-java, after Andreas imported the last upstream version. This package builds a java package with a .jar file and a jni package with native code used by the .jar. I have been able to: - refresh patches; - get rid of the private header H5private.h of source package hdf5, which is not shipped by any package. Only a few simple preprocessor directives of that file were used; - update the list of build-depends; - have the package build, including the override of dh_auto_test that caused issues previously. Yet: - it seems that only a few upstream-provided tests are run in dh_auto_test, so having the build complete is maybe not so meaningful :-( ; - I have begun designing tests for the autopkgtest testsuite, using upstream-provided tests, and while around 30 of them pass, there remains a lot of failing tests. It seems that the linking of the jni with the jar is not correctly done at build-time. At that point I would need help, as this package is complicated: the build processes of the jar and the jni are somehow entangled and I do not have enough knowledge of Java packaging to be able to solve the issues I'm facing. Maybe there does not remain so much to be done; if someone has Java knowledge and could look to the current packaging I have put into Salsa [1], this would be really great. Thank you and have a good week, All the best, Pierre [1] https://salsa.debian.org/med-team/libsis-jhdf5-java
Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
On Tue, Apr 28, 2020 at 4:31 PM Andreas Tille wrote: > > Hi Ben, > > On Tue, Apr 28, 2020 at 03:16:56PM +0200, Ben Tris wrote: > > I am willing to ask about guppy first, > > Thanks a lot. Thanks! > > but what address could I use best? > > May be you can check out the links Michael has given. Does anybody > have some other points of contact? I personally have no idea, sorry. > > > And I'm afraid that I will not be that convincing, don't know the > > exact use and needs for having guppy freed. > > I'd start with the fact that guppy is on our list of software that > is relevant to fight COVID-19. At the end of our wiki page > >https://wiki.debian.org/DebianMed/SoftwareLiberation The information comes from the talk in nf-core Slack #covid19 channel. Here is the link. If you join the Slack, maybe you can see it. https://nfcore.slack.com/archives/C0105J0J9T8/p1587416769052300 > I can see nf-core/artic, nf-core/viralrecon, nf-core/nanoseq are used for > that. > ... > The pipelines you listed are the ones that are/will be most applicable to > COVID-19 analysis nf-core/nanoseq project includes guppy as a dependency. -- Jun | He - His - Him
Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
Hi Ben, On Tue, Apr 28, 2020 at 03:16:56PM +0200, Ben Tris wrote: > I am willing to ask about guppy first, Thanks a lot. > but what address could I use best? May be you can check out the links Michael has given. Does anybody have some other points of contact? I personally have no idea, sorry. > And I'm afraid that I will not be that convincing, don't know the > exact use and needs for having guppy freed. I'd start with the fact that guppy is on our list of software that is relevant to fight COVID-19. At the end of our wiki page https://wiki.debian.org/DebianMed/SoftwareLiberation is a nice link about kallisto featuring good arguments. Hope this helps Andreas. > On 28-04-20 15:11, Andreas Tille wrote: > > Hi Ben, > > > > would you volunteer to contact the authors about this? > > > > Thanks a lot in advance > > > > Andreas. > > > > On Tue, Apr 28, 2020 at 03:01:51PM +0200, Ben Tris wrote: > >> I was referring to the flappy license, that is mozilla like > >> maybe they are willing to change to MPL-2.0 that is GPL compatible > >> if that research only is a problem, but I think (guess) there are > >> enough escapes in the license. > >> > >> I still think there should be a confirmation > >> that guppy will not be available with a free software > >> license. Because I think it is developed with > >> contributions from the community. > >> > >> Otherwise it is indeed non-free. > >> > >> Based on the flappy license, should asked to release guppy with MPL-2.0? > >> > >> Someone mentioned chiron, maybe that is the only good alternative at > >> this moment? > >> (the Basecalling-comparison contains some additional advice on chiron > >> settings) > >> > >> On 28-04-20 10:11, Andreas Tille wrote: > >>> Hi Michael, > >>> > >>> thanks a lot for the links. Any volunteer to start some discussion? > >>> As I said: If we do not try nothing will change. People with no > >>> technical skills could contribute by doing so to take some workload > >>> from packagers. > >>> > >>> I'll offer a $DRINK at next Debian Med sprint for every attempt to > >>> change a license. ;-) > >>> > >>> Kind regards > >>> > >>> Andreas. > >>> > >>> On Tue, Apr 28, 2020 at 09:30:06AM +0200, Michael Crusoe wrote: > The guppy binary license is > https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf > No source code is provided. No competitors of the company may use the > software. Must be for "research use only". > > https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt > "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used > to > license some of their "source available" software > Only permits "research purposes", violating DFSG guideline #6 "No > Discrimination Against Fields of Endeavor" > > https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the > Mozilla > Public License and is DFSG compatible > > On Mon, Apr 27, 2020 at 6:40 PM Ben Tris wrote: > > > Sorry to pop in. > > I think this license should be reviewed, > > unless sure it is not a free license. > > To me it looks like a free software license. > > Although not understand most. > > > > What is making this license non-free? > > > > On 27-04-20 17:06, Jun Aruga wrote: > >> On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille wrote: > >>> Hi again, > >>> > >>> this brings up again my point: We *really*, *really* should take the > >>> chance right now to ask upstreams for free licensing. The time is > >>> good. > >>> We just need somebody who is really doing this. > >> For us, the free licensing is good. But for the company nanopore > >> technologies it is their core competency. > >> I am not sure we can make it happen, but it might be worth trying to > >> ask. > >> > >>> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote: > Extracting the linked deb, one finds a binary and a very restrictive > license. I do not believe that guppy source code is available nor it > is > likely to become available any time soon. > > While some of their other basecallers have source code available, I > > would > not call the license OSS: > https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt > >> I found guppy client software that might be an alternative to use > >> guppy's function. > >> https://github.com/nanoporetech/pyguppyclient > >> > >> As Michael mentioned, checking other basecallers for nanopore, then > >> communicating the nf-core/nanoseq project using the alternative base > >> caller optionally. > >> > >> I found an interesting document about the basecallers. > >> https://github.com/rrwick/Basecalling-comparison > >> > >> Performance of neural network
Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
Hi Ben, would you volunteer to contact the authors about this? Thanks a lot in advance Andreas. On Tue, Apr 28, 2020 at 03:01:51PM +0200, Ben Tris wrote: > I was referring to the flappy license, that is mozilla like > maybe they are willing to change to MPL-2.0 that is GPL compatible > if that research only is a problem, but I think (guess) there are > enough escapes in the license. > > I still think there should be a confirmation > that guppy will not be available with a free software > license. Because I think it is developed with > contributions from the community. > > Otherwise it is indeed non-free. > > Based on the flappy license, should asked to release guppy with MPL-2.0? > > Someone mentioned chiron, maybe that is the only good alternative at > this moment? > (the Basecalling-comparison contains some additional advice on chiron > settings) > > On 28-04-20 10:11, Andreas Tille wrote: > > Hi Michael, > > > > thanks a lot for the links. Any volunteer to start some discussion? > > As I said: If we do not try nothing will change. People with no > > technical skills could contribute by doing so to take some workload > > from packagers. > > > > I'll offer a $DRINK at next Debian Med sprint for every attempt to > > change a license. ;-) > > > > Kind regards > > > > Andreas. > > > > On Tue, Apr 28, 2020 at 09:30:06AM +0200, Michael Crusoe wrote: > >> The guppy binary license is > >> https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf > >> No source code is provided. No competitors of the company may use the > >> software. Must be for "research use only". > >> > >> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt > >> "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to > >> license some of their "source available" software > >> Only permits "research purposes", violating DFSG guideline #6 "No > >> Discrimination Against Fields of Endeavor" > >> > >> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla > >> Public License and is DFSG compatible > >> > >> On Mon, Apr 27, 2020 at 6:40 PM Ben Tris wrote: > >> > >>> Sorry to pop in. > >>> I think this license should be reviewed, > >>> unless sure it is not a free license. > >>> To me it looks like a free software license. > >>> Although not understand most. > >>> > >>> What is making this license non-free? > >>> > >>> On 27-04-20 17:06, Jun Aruga wrote: > On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille wrote: > > Hi again, > > > > this brings up again my point: We *really*, *really* should take the > > chance right now to ask upstreams for free licensing. The time is good. > > We just need somebody who is really doing this. > For us, the free licensing is good. But for the company nanopore > technologies it is their core competency. > I am not sure we can make it happen, but it might be worth trying to ask. > > > On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote: > >> Extracting the linked deb, one finds a binary and a very restrictive > >> license. I do not believe that guppy source code is available nor it is > >> likely to become available any time soon. > >> > >> While some of their other basecallers have source code available, I > >>> would > >> not call the license OSS: > >> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt > I found guppy client software that might be an alternative to use > guppy's function. > https://github.com/nanoporetech/pyguppyclient > > As Michael mentioned, checking other basecallers for nanopore, then > communicating the nf-core/nanoseq project using the alternative base > caller optionally. > > I found an interesting document about the basecallers. > https://github.com/rrwick/Basecalling-comparison > > Performance of neural network basecalling tools for Oxford Nanopore > >>> sequencing > >>> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y > > In this study, we tested four basecalling programs developed by ONT – > >>> Albacore, Guppy, Scrappie and Flappie > > ... > > We also tested Chiron (https://github.com/haotianteng/Chiron), a > >>> third-party basecaller still under development that uses a deeper neural > >>> network than ONT’s basecallers [3]. > The third party basecaller Chiron's license is Mozilla Public License, > >>> v. 2.0. > https://github.com/haotianteng/Chiron/blob/master/LICENSE.md > > >>> > >> -- > >> Michael R. Crusoe > -- http://fam-tille.de
Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
I am willing to ask about guppy first, but what address could I use best? And I'm afraid that I will not be that convincing, don't know the exact use and needs for having guppy freed. On 28-04-20 15:11, Andreas Tille wrote: > Hi Ben, > > would you volunteer to contact the authors about this? > > Thanks a lot in advance > > Andreas. > > On Tue, Apr 28, 2020 at 03:01:51PM +0200, Ben Tris wrote: >> I was referring to the flappy license, that is mozilla like >> maybe they are willing to change to MPL-2.0 that is GPL compatible >> if that research only is a problem, but I think (guess) there are >> enough escapes in the license. >> >> I still think there should be a confirmation >> that guppy will not be available with a free software >> license. Because I think it is developed with >> contributions from the community. >> >> Otherwise it is indeed non-free. >> >> Based on the flappy license, should asked to release guppy with MPL-2.0? >> >> Someone mentioned chiron, maybe that is the only good alternative at >> this moment? >> (the Basecalling-comparison contains some additional advice on chiron >> settings) >> >> On 28-04-20 10:11, Andreas Tille wrote: >>> Hi Michael, >>> >>> thanks a lot for the links. Any volunteer to start some discussion? >>> As I said: If we do not try nothing will change. People with no >>> technical skills could contribute by doing so to take some workload >>> from packagers. >>> >>> I'll offer a $DRINK at next Debian Med sprint for every attempt to >>> change a license. ;-) >>> >>> Kind regards >>> >>> Andreas. >>> >>> On Tue, Apr 28, 2020 at 09:30:06AM +0200, Michael Crusoe wrote: The guppy binary license is https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf No source code is provided. No competitors of the company may use the software. Must be for "research use only". https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to license some of their "source available" software Only permits "research purposes", violating DFSG guideline #6 "No Discrimination Against Fields of Endeavor" https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla Public License and is DFSG compatible On Mon, Apr 27, 2020 at 6:40 PM Ben Tris wrote: > Sorry to pop in. > I think this license should be reviewed, > unless sure it is not a free license. > To me it looks like a free software license. > Although not understand most. > > What is making this license non-free? > > On 27-04-20 17:06, Jun Aruga wrote: >> On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille wrote: >>> Hi again, >>> >>> this brings up again my point: We *really*, *really* should take the >>> chance right now to ask upstreams for free licensing. The time is good. >>> We just need somebody who is really doing this. >> For us, the free licensing is good. But for the company nanopore >> technologies it is their core competency. >> I am not sure we can make it happen, but it might be worth trying to ask. >> >>> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote: Extracting the linked deb, one finds a binary and a very restrictive license. I do not believe that guppy source code is available nor it is likely to become available any time soon. While some of their other basecallers have source code available, I > would not call the license OSS: https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt >> I found guppy client software that might be an alternative to use >> guppy's function. >> https://github.com/nanoporetech/pyguppyclient >> >> As Michael mentioned, checking other basecallers for nanopore, then >> communicating the nf-core/nanoseq project using the alternative base >> caller optionally. >> >> I found an interesting document about the basecallers. >> https://github.com/rrwick/Basecalling-comparison >> >> Performance of neural network basecalling tools for Oxford Nanopore > sequencing > https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y >>> In this study, we tested four basecalling programs developed by ONT – > Albacore, Guppy, Scrappie and Flappie >>> ... >>> We also tested Chiron (https://github.com/haotianteng/Chiron), a > third-party basecaller still under development that uses a deeper neural > network than ONT’s basecallers [3]. >> The third party basecaller Chiron's license is Mozilla Public License, > v. 2.0. >> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md >> -- Michael R. Crusoe > > > signature.asc Description: OpenPGP digital signature
Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
I was referring to the flappy license, that is mozilla like maybe they are willing to change to MPL-2.0 that is GPL compatible if that research only is a problem, but I think (guess) there are enough escapes in the license. I still think there should be a confirmation that guppy will not be available with a free software license. Because I think it is developed with contributions from the community. Otherwise it is indeed non-free. Based on the flappy license, should asked to release guppy with MPL-2.0? Someone mentioned chiron, maybe that is the only good alternative at this moment? (the Basecalling-comparison contains some additional advice on chiron settings) On 28-04-20 10:11, Andreas Tille wrote: > Hi Michael, > > thanks a lot for the links. Any volunteer to start some discussion? > As I said: If we do not try nothing will change. People with no > technical skills could contribute by doing so to take some workload > from packagers. > > I'll offer a $DRINK at next Debian Med sprint for every attempt to > change a license. ;-) > > Kind regards > > Andreas. > > On Tue, Apr 28, 2020 at 09:30:06AM +0200, Michael Crusoe wrote: >> The guppy binary license is >> https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf >> No source code is provided. No competitors of the company may use the >> software. Must be for "research use only". >> >> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt >> "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to >> license some of their "source available" software >> Only permits "research purposes", violating DFSG guideline #6 "No >> Discrimination Against Fields of Endeavor" >> >> https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla >> Public License and is DFSG compatible >> >> On Mon, Apr 27, 2020 at 6:40 PM Ben Tris wrote: >> >>> Sorry to pop in. >>> I think this license should be reviewed, >>> unless sure it is not a free license. >>> To me it looks like a free software license. >>> Although not understand most. >>> >>> What is making this license non-free? >>> >>> On 27-04-20 17:06, Jun Aruga wrote: On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille wrote: > Hi again, > > this brings up again my point: We *really*, *really* should take the > chance right now to ask upstreams for free licensing. The time is good. > We just need somebody who is really doing this. For us, the free licensing is good. But for the company nanopore technologies it is their core competency. I am not sure we can make it happen, but it might be worth trying to ask. > On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote: >> Extracting the linked deb, one finds a binary and a very restrictive >> license. I do not believe that guppy source code is available nor it is >> likely to become available any time soon. >> >> While some of their other basecallers have source code available, I >>> would >> not call the license OSS: >> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt I found guppy client software that might be an alternative to use guppy's function. https://github.com/nanoporetech/pyguppyclient As Michael mentioned, checking other basecallers for nanopore, then communicating the nf-core/nanoseq project using the alternative base caller optionally. I found an interesting document about the basecallers. https://github.com/rrwick/Basecalling-comparison Performance of neural network basecalling tools for Oxford Nanopore >>> sequencing >>> https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y > In this study, we tested four basecalling programs developed by ONT – >>> Albacore, Guppy, Scrappie and Flappie > ... > We also tested Chiron (https://github.com/haotianteng/Chiron), a >>> third-party basecaller still under development that uses a deeper neural >>> network than ONT’s basecallers [3]. The third party basecaller Chiron's license is Mozilla Public License, >>> v. 2.0. https://github.com/haotianteng/Chiron/blob/master/LICENSE.md >>> >> -- >> Michael R. Crusoe signature.asc Description: OpenPGP digital signature
[covid-19] Gradle help for nextflow needed
Hi, in our COVID-19 effort the Debian Med team intends to package some workflows that are useful to detect viruses. A common workflow tool is nextflow which I in injected into Salsa[1]. The build system uses gradle where I do not have any experience in. The build log of my weak attempt is running into: ... Evaluating root project 'nextflow-prj' using build file '/build/nextflow-20.04.1-edge/build.gradle'. Compiling build file '/build/nextflow-20.04.1-edge/build.gradle' using SubsetScriptTransformer. Creating new cache for metadata-2.36/module-metadata, path /build/nextflow-20.04.1-edge/.gradle/caches/modules-2/metadata-2.36/module-metadata.bin, access org.gradle.cache.internal.DefaultCacheAccess@19705650 FAILURE: Build failed with an exception. * Where: Build file '/build/nextflow-20.04.1-edge/build.gradle' line: 18 * What went wrong: Plugin [id: 'io.codearte.nexus-staging', version: '0.21.2'] was not found in any of the following sources: - Gradle Core Plugins (plugin is not in 'org.gradle' namespace) - Plugin Repositories (could not resolve plugin artifact 'io.codearte.nexus-staging:io.codearte.nexus-staging.gradle.plugin:0.21.2') Searched in the following repositories: Gradle Central Plugin Repository * Try: Run with --debug option to get more log output. Run with --scan to get full insights. * Exception is: org.gradle.api.plugins.UnknownPluginException: Plugin [id: 'io.codearte.nexus-staging', version: '0.21.2'] was not found in any of the following sources: - Gradle Core Plugins (plugin is not in 'org.gradle' namespace) - Plugin Repositories (could not resolve plugin artifact 'io.codearte.nexus-staging:io.codearte.nexus-staging.gradle.plugin:0.21.2') Searched in the following repositories: Gradle Central Plugin Repository at org.gradle.plugin.use.internal.DefaultPluginRequestApplicator.resolveToFoundResult(DefaultPluginRequestApplicator.java:262) at org.gradle.plugin.use.internal.DefaultPluginRequestApplicator.access$100(DefaultPluginRequestApplicator.java:63) at org.gradle.plugin.use.internal.DefaultPluginRequestApplicator$1.transform(DefaultPluginRequestApplicator.java:91) at org.gradle.plugin.use.internal.DefaultPluginRequestApplicator$1.transform(DefaultPluginRequestApplicator.java:88) at org.gradle.util.CollectionUtils.collect(CollectionUtils.java:203) at org.gradle.util.CollectionUtils.collect(CollectionUtils.java:198) ... Any help for a kickstart would be really appreciated. Kind regards Andreas. [1] https://salsa.debian.org/med-team/nextflow -- http://fam-tille.de
Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
Hi Michael, thanks a lot for the links. Any volunteer to start some discussion? As I said: If we do not try nothing will change. People with no technical skills could contribute by doing so to take some workload from packagers. I'll offer a $DRINK at next Debian Med sprint for every attempt to change a license. ;-) Kind regards Andreas. On Tue, Apr 28, 2020 at 09:30:06AM +0200, Michael Crusoe wrote: > The guppy binary license is > https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf > No source code is provided. No competitors of the company may use the > software. Must be for "research use only". > > https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt > "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to > license some of their "source available" software > Only permits "research purposes", violating DFSG guideline #6 "No > Discrimination Against Fields of Endeavor" > > https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla > Public License and is DFSG compatible > > On Mon, Apr 27, 2020 at 6:40 PM Ben Tris wrote: > > > Sorry to pop in. > > I think this license should be reviewed, > > unless sure it is not a free license. > > To me it looks like a free software license. > > Although not understand most. > > > > What is making this license non-free? > > > > On 27-04-20 17:06, Jun Aruga wrote: > > > On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille wrote: > > >> Hi again, > > >> > > >> this brings up again my point: We *really*, *really* should take the > > >> chance right now to ask upstreams for free licensing. The time is good. > > >> We just need somebody who is really doing this. > > > For us, the free licensing is good. But for the company nanopore > > > technologies it is their core competency. > > > I am not sure we can make it happen, but it might be worth trying to ask. > > > > > >> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote: > > >>> Extracting the linked deb, one finds a binary and a very restrictive > > >>> license. I do not believe that guppy source code is available nor it is > > >>> likely to become available any time soon. > > >>> > > >>> While some of their other basecallers have source code available, I > > would > > >>> not call the license OSS: > > >>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt > > > I found guppy client software that might be an alternative to use > > > guppy's function. > > > https://github.com/nanoporetech/pyguppyclient > > > > > > As Michael mentioned, checking other basecallers for nanopore, then > > > communicating the nf-core/nanoseq project using the alternative base > > > caller optionally. > > > > > > I found an interesting document about the basecallers. > > > https://github.com/rrwick/Basecalling-comparison > > > > > > Performance of neural network basecalling tools for Oxford Nanopore > > sequencing > > > > > https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y > > > > > >> In this study, we tested four basecalling programs developed by ONT – > > Albacore, Guppy, Scrappie and Flappie > > >> ... > > >> We also tested Chiron (https://github.com/haotianteng/Chiron), a > > third-party basecaller still under development that uses a deeper neural > > network than ONT’s basecallers [3]. > > > The third party basecaller Chiron's license is Mozilla Public License, > > v. 2.0. > > > https://github.com/haotianteng/Chiron/blob/master/LICENSE.md > > > > > > > > > -- > Michael R. Crusoe -- http://fam-tille.de
Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
The guppy binary license is https://nanoporetech.com/sites/default/files/s3/terms/Nanopore-product-terms-and-conditions-nov2018-v2.pdf No source code is provided. No competitors of the company may use the software. Must be for "research use only". https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt "Oxford Nanopore Technologies, Ltd. Public License Version 1.0" is used to license some of their "source available" software Only permits "research purposes", violating DFSG guideline #6 "No Discrimination Against Fields of Endeavor" https://github.com/haotianteng/Chiron/blob/master/LICENSE.md is the Mozilla Public License and is DFSG compatible On Mon, Apr 27, 2020 at 6:40 PM Ben Tris wrote: > Sorry to pop in. > I think this license should be reviewed, > unless sure it is not a free license. > To me it looks like a free software license. > Although not understand most. > > What is making this license non-free? > > On 27-04-20 17:06, Jun Aruga wrote: > > On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille wrote: > >> Hi again, > >> > >> this brings up again my point: We *really*, *really* should take the > >> chance right now to ask upstreams for free licensing. The time is good. > >> We just need somebody who is really doing this. > > For us, the free licensing is good. But for the company nanopore > > technologies it is their core competency. > > I am not sure we can make it happen, but it might be worth trying to ask. > > > >> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote: > >>> Extracting the linked deb, one finds a binary and a very restrictive > >>> license. I do not believe that guppy source code is available nor it is > >>> likely to become available any time soon. > >>> > >>> While some of their other basecallers have source code available, I > would > >>> not call the license OSS: > >>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt > > I found guppy client software that might be an alternative to use > > guppy's function. > > https://github.com/nanoporetech/pyguppyclient > > > > As Michael mentioned, checking other basecallers for nanopore, then > > communicating the nf-core/nanoseq project using the alternative base > > caller optionally. > > > > I found an interesting document about the basecallers. > > https://github.com/rrwick/Basecalling-comparison > > > > Performance of neural network basecalling tools for Oxford Nanopore > sequencing > > > https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y > > > >> In this study, we tested four basecalling programs developed by ONT – > Albacore, Guppy, Scrappie and Flappie > >> ... > >> We also tested Chiron (https://github.com/haotianteng/Chiron), a > third-party basecaller still under development that uses a deeper neural > network than ONT’s basecallers [3]. > > The third party basecaller Chiron's license is Mozilla Public License, > v. 2.0. > > https://github.com/haotianteng/Chiron/blob/master/LICENSE.md > > > > -- Michael R. Crusoe
Re: Help for asking upstreams about free licenses urgently needed (Was: Help: Seeking source code of guppy base caller)
On Mon, Apr 27, 2020 at 06:39:44PM +0200, Ben Tris wrote: > Sorry to pop in. > I think this license should be reviewed, What exact license are you talking about. I'm missing a link to guppy source code including any license. > unless sure it is not a free license. > To me it looks like a free software license. Which one are you talking about? Kind regards Andreas. > Although not understand most. > > What is making this license non-free? > > On 27-04-20 17:06, Jun Aruga wrote: > > On Mon, Apr 27, 2020 at 4:43 PM Andreas Tille wrote: > >> Hi again, > >> > >> this brings up again my point: We *really*, *really* should take the > >> chance right now to ask upstreams for free licensing. The time is good. > >> We just need somebody who is really doing this. > > For us, the free licensing is good. But for the company nanopore > > technologies it is their core competency. > > I am not sure we can make it happen, but it might be worth trying to ask. > > > >> On Mon, Apr 27, 2020 at 04:21:12PM +0200, Michael Crusoe wrote: > >>> Extracting the linked deb, one finds a binary and a very restrictive > >>> license. I do not believe that guppy source code is available nor it is > >>> likely to become available any time soon. > >>> > >>> While some of their other basecallers have source code available, I would > >>> not call the license OSS: > >>> https://github.com/nanoporetech/flappie/blob/master/LICENCE.txt > > I found guppy client software that might be an alternative to use > > guppy's function. > > https://github.com/nanoporetech/pyguppyclient > > > > As Michael mentioned, checking other basecallers for nanopore, then > > communicating the nf-core/nanoseq project using the alternative base > > caller optionally. > > > > I found an interesting document about the basecallers. > > https://github.com/rrwick/Basecalling-comparison > > > > Performance of neural network basecalling tools for Oxford Nanopore > > sequencing > > https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1727-y > > > >> In this study, we tested four basecalling programs developed by ONT – > >> Albacore, Guppy, Scrappie and Flappie > >> ... > >> We also tested Chiron (https://github.com/haotianteng/Chiron), a > >> third-party basecaller still under development that uses a deeper neural > >> network than ONT’s basecallers [3]. > > The third party basecaller Chiron's license is Mozilla Public License, v. > > 2.0. > > https://github.com/haotianteng/Chiron/blob/master/LICENSE.md > > > -- http://fam-tille.de
