Steffen Möller pushed to branch master at Debian Med / minia
Commits: 6b22ed14 by Steffen Moeller at 2021-02-16T16:14:36+01:00 Wording. Added myself to uploaders. - - - - - e30eaf4e by Steffen Moeller at 2021-02-16T19:33:20+01:00 Adjust dep to patched version of gatb - - - - - 4 changed files: - debian/changelog - debian/control - debian/rules - debian/watch Changes: ===================================== debian/changelog ===================================== @@ -3,14 +3,10 @@ minia (3.2.4-1) UNRELEASED; urgency=medium * Team upload. * New upstream version * debhelper-compat 13 (routine-update) + * Adjusted build dependencies to patched version of gatb 1.4.2 + * d/rules - improved clean * d/watch - using regular releases again (up from 3.2.1 to 3.2.4) - BLOCKER: FTBFS needs new gatb version - /usr/include/gatb/tools/math/Integer.hpp:84:71: required from ‘static void gatb::core::tools::math::IntegerTemplate<IntegerList>::apply(size_t, Parameter) [with Functor = MiniaFunctor; Parameter = Parameter; IntegerList = boost::mpl::vector4<mpl_::int_<32>, mpl_::int_<64>, mpl_::int_<96>, mpl_::int_<128> >; size_t = long unsigned int]’ - /med-team/minia/src/Minia.cpp:170:65: required from here - /med-team/minia/src/Minia.cpp:312:62: error: ‘class gatb::core::debruijn::impl::GraphUnitigsTemplate<128>’ has no member named ‘_nbSolidKmers’ - - -- Steffen Moeller <[email protected]> Mon, 10 Aug 2020 19:16:26 +0200 minia (3.2.1+git20200522.4960a99-1) unstable; urgency=medium ===================================== debian/control ===================================== @@ -1,7 +1,8 @@ Source: minia Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Olivier Sallou <[email protected]>, - Andreas Tille <[email protected]> + Andreas Tille <[email protected]>, + Steffen Moeller <[email protected]> Section: science Priority: optional Build-Depends: debhelper-compat (= 13), @@ -9,9 +10,9 @@ Build-Depends: debhelper-compat (= 13), bc, zlib1g-dev, libboost-dev, - libgatbcore-dev (>= 1.4.1+git20191130.664696c), + libgatbcore-dev (>= 1.4.2-7), libhdf5-dev -Standards-Version: 4.5.0 +Standards-Version: 4.5.1 Vcs-Browser: https://salsa.debian.org/med-team/minia Vcs-Git: https://salsa.debian.org/med-team/minia.git Homepage: http://minia.genouest.org/ @@ -26,9 +27,21 @@ Depends: ${misc:Depends}, Recommends: samtools Suggests: bandage Description: short-read biological sequence assembler - Short-read DNA sequence assembler based on a de Bruijn graph, - capable of assembling a human genome on a desktop computer in a day. + What was referred to as "next-generation" DNA sequencing up to + the year 2020 delivered only "short" reads up to ~600 base pairs + in length that would then have to be puzzled by random overlaps + in their sequence towards a complete genome. This is the genome + assembly. And there are many biological pitfalls on long stretches + of low complexity regions and copy number variations and other + sorts of redundancies that render this difficult. + . + This package provides a short-read DNA sequence assembler based on a + de Bruijn graph, capable of assembling a human genome on a desktop + computer in a day. + . + The output of Minia is a set of contigs, i.e. stretches of gap-free + linear overlaps of short reads. In the best possible case this is + a whole chromosome. . - The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet). ===================================== debian/rules ===================================== @@ -11,3 +11,4 @@ export DEB_BUILD_MAINT_OPTIONS=hardening=+all override_dh_clean: dh_clean rm -f minia src/build_info.hpp + rm -rf obj-x86_64-linux-gnu src/build_info.hpp ===================================== debian/watch ===================================== @@ -3,6 +3,6 @@ version=4 https://github.com/GATB/minia/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) # Once upon a time, the released version was not compatible with gatb-core 1.4.1+git20191130.664696c+dfsg -# That is we sticked to latest Git commit back then. +# That is why we sticked to latest Git commit back then. #opts="mode=git,pretty=3.2.1+git%cd.%h" \ # https://github.com/GATB/minia.git HEAD View it on GitLab: https://salsa.debian.org/med-team/minia/-/compare/0eaa42246bcb41e6d6f7e13e8e08e1f8f3dcb0ee...e30eaf4e8d414d7080712ce424c266f8ece3bdfd -- View it on GitLab: https://salsa.debian.org/med-team/minia/-/compare/0eaa42246bcb41e6d6f7e13e8e08e1f8f3dcb0ee...e30eaf4e8d414d7080712ce424c266f8ece3bdfd You're receiving this email because of your account on salsa.debian.org.
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