Hi Nilesh, Nilesh Patra, on 2022-07-24: > On 7/24/22 12:55 PM, Étienne Mollier wrote: > > * Is it still worth testing/fixing truspades, given that > > getting it sorted does not look very obvious on first sight, > > or should I just comment out truspades self-test in the > > autopkgtest? > > If it is unsupported then it probably isn't worth our time either. Thank you for your suggestion, it makes sense. In that case, I consider running the self-test, but just outputing a warning when the command fails them. > > * Should I drop a NEWS item to notify end users? > > While it gives a warning, IMHO it still does not hurt to add in a NEWS entry to > notify the users. Current draft NEWS entry looks like the below; I'm sure there is room for improvement: -------8<--------------8<--------------8<--------------8<------- spades (3.15.5+dfsg-1) UNRELEASED; urgency=medium Since version 3.15, the truspades command is deprecated. According to upstream[1], the technology behind truspades is a thing of the past: > Thanks for the report. truSPAdes is not maintained anymore for many reasons > (the technology is dead, etc.), so these issues will likely be fixed in > radical way when truSPAdes will be deprecated and removed [1]: https://github.com/ablab/spades/issues/560#issuecomment-675915841 It is quite possible that the truspades version still provided by Debian Med is not working well anymore. At least it has been noticed that it failed its self-test since version 3.15.5. The test fails by not outputting the assemble scaffolds file then supposed to be processed by the `bwa` program in the sample workflow. The command truspades will probably not make it beyond spades version 3.16. -- Étienne Mollier <emollier@debian.org> Sun, 24 Jul 2022 16:05:54 +0200 ------->8-------------->8-------------->8-------------->8------- I'm a bit concerned that there are no ways to replace the command by something else, but I assume truspades is going away for good reasons. > PS: I am not a user of the package, but only suggesting here. Neither am I a spades user, for the record. I'm taker of further details on the topic if someone is from the field. Have a nice day, :) -- .''`. Étienne Mollier <emollier@debian.org> : :' : gpg: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da `. `' sent from /dev/pts/3, please excuse my verbosity `-
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