Étienne Mollier pushed to branch master at Debian Med / spades
Commits: 9304c2be by Étienne Mollier at 2022-07-24T13:35:19+02:00 d/m/coronaspades.1.adoc: add manual page for coronaspades. - - - - - 446da7df by Étienne Mollier at 2022-07-24T16:05:29+02:00 d/t/run-upstreams-tests: update to current binaries. Notably, the truspades command is deprecated, so don't make it's self-test failure critical. - - - - - ccdca122 by Étienne Mollier at 2022-07-24T16:21:09+02:00 d/links: create link for coronaspades.py manual. - - - - - ed5eacb0 by Étienne Mollier at 2022-07-24T17:34:51+02:00 NEWS: drafted entry about truspades deprecation. - - - - - bb3eeb69 by Étienne Mollier at 2022-07-24T17:38:16+02:00 update changelog, with notice about finishing NEWS - - - - - 5 changed files: - + debian/NEWS - debian/changelog - debian/links - + debian/man_src/coronaspades.1.adoc - debian/tests/run-upstreams-tests Changes: ===================================== debian/NEWS ===================================== @@ -0,0 +1,20 @@ +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 <[email protected]> Sun, 24 Jul 2022 16:05:54 +0200 ===================================== debian/changelog ===================================== @@ -1,13 +1,19 @@ spades (3.15.5+dfsg-1) UNRELEASED; urgency=medium + TODO: NEWS: drafted entry about truspades deprecation, need polishing. * New upstream version 3.15.5+dfsg * d/patches/: + fix-privacy-breaches.patch: update badges list. + python3.patch: refresh. + 0003_accept-system-bwa.patch: unfuzz. + yaml_load.patch: unfuzz. + * d/m/coronaspades.1.adoc: add manual page for coronaspades. + * d/links: create a link for coronaspades.py manual. + * d/t/run-upstreams-tests: add self tests for plasmidspades and coronaspades. + Also, the truspades command is deprecated, so don't make it's self-test + failure critical. - -- Étienne Mollier <[email protected]> Sun, 24 Jul 2022 07:41:58 +0200 + -- Étienne Mollier <[email protected]> Sun, 24 Jul 2022 17:35:37 +0200 spades (3.15.4+dfsg-3) unstable; urgency=medium ===================================== debian/links ===================================== @@ -15,4 +15,5 @@ usr/share/man/man1/truspades.1.gz /usr/share/man/man1/truspades.py.1.gz usr/share/man/man1/metaspades.1.gz /usr/share/man/man1/metaspades.py.1.gz usr/share/man/man1/plasmidspades.1.gz /usr/share/man/man1/plasmidspades.py.1.gz usr/share/man/man1/rnaspades.1.gz /usr/share/man/man1/rnaspades.py.1.gz +usr/share/man/man1/coronaspades.1.gz /usr/share/man/man1/coronaspades.py.1.gz usr/share/spades/VERSION usr/libexec/spades/VERSION ===================================== debian/man_src/coronaspades.1.adoc ===================================== @@ -0,0 +1,18 @@ += coronaspades(1) + +## NAME + +coronaspades - SPAdes genome assembler (coronaSPAdes mode) + +## SYNOPSIS + +*coronaspades* [options] -o <output_dir> + +## DESCRIPTION + +*coronaspades* runs **SPAdes** in coronaSPAdes mode. All parameters are +identical to the regular SPAdes. + +## SEE ALSO + +spades(1) ===================================== debian/tests/run-upstreams-tests ===================================== @@ -8,6 +8,17 @@ trap "rm -rf $WORKDIR" 0 INT QUIT ABRT PIPE TERM cd $WORKDIR spades --test -truspades --test +coronaspades --test metaspades --test +plasmidspades --test rnaspades --test + +# truspades is deprecated in v3.15 and may fail its own test suite. +if command -v truspades > /dev/null +then + if ! truspades --test + then echo 'W: truspades failed its self-test suite.' + fi +else + echo 'W: truspades is not provided upstream anymore.' +fi View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/fbfcea010aef8ce5bd51ae473a8e6e7bee66b7c9...bb3eeb69b86200c3762d00ed8db339f2fb782912 -- View it on GitLab: https://salsa.debian.org/med-team/spades/-/compare/fbfcea010aef8ce5bd51ae473a8e6e7bee66b7c9...bb3eeb69b86200c3762d00ed8db339f2fb782912 You're receiving this email because of your account on salsa.debian.org.
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