[med-svn] [Git][med-team/minia][master] 2 commits: Wording. Added myself to uploaders.

[Steffen Möller]

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 <moeller at debian.org>  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 <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Olivier Sallou <osallou at debian.org>,
-           Andreas Tille <tille at debian.org>
+           Andreas Tille <tille at debian.org>,
+           Steffen Moeller <moeller at debian.org>
 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
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