commit: f22bb3be4e8f283831edc5f4c38a839442355644 Author: Martin Mokrejs <mmokrejs <AT> gmail <DOT> com> AuthorDate: Wed Apr 14 13:07:12 2021 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> CommitDate: Wed Apr 14 13:07:12 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f22bb3be
sci-biology/abyss: fix PathConsensus crashes Fixes: https://github.com/bcgsc/abyss/issues/267 Fix crashes of PathConsensus during long-scaffolding step per @sjackman suggestions. Add back 2.2.5 version which does not have yet the RResolver which addition broke the paired de Bruijn graph assembly approach and since that only the Bloom filter-based approach works in 2.3.0. Package-Manager: Portage-3.0.18, Repoman-3.0.3 Signed-off-by: Martin Mokrejs <mmokrejs <AT> gmail.com> .../abyss/{abyss-2.3.0.ebuild => abyss-2.2.5-r1.ebuild} | 4 ++++ .../abyss/{abyss-2.3.0.ebuild => abyss-2.3.0-r1.ebuild} | 4 ++++ sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch | 11 +++++++++++ .../abyss/files/abyss-2.2.5-PathConsensus-assert.patch | 11 +++++++++++ 4 files changed, 30 insertions(+) diff --git a/sci-biology/abyss/abyss-2.3.0.ebuild b/sci-biology/abyss/abyss-2.2.5-r1.ebuild similarity index 91% copy from sci-biology/abyss/abyss-2.3.0.ebuild copy to sci-biology/abyss/abyss-2.2.5-r1.ebuild index 95438d3b4..d9134813b 100644 --- a/sci-biology/abyss/abyss-2.3.0.ebuild +++ b/sci-biology/abyss/abyss-2.2.5-r1.ebuild @@ -27,6 +27,10 @@ DEPEND="${RDEPEND} dev-lang/ghc )" +PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch + "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch + ) + # todo: --enable-maxk=N configure option # todo: fix automagic mpi toggling diff --git a/sci-biology/abyss/abyss-2.3.0.ebuild b/sci-biology/abyss/abyss-2.3.0-r1.ebuild similarity index 91% rename from sci-biology/abyss/abyss-2.3.0.ebuild rename to sci-biology/abyss/abyss-2.3.0-r1.ebuild index 95438d3b4..d9134813b 100644 --- a/sci-biology/abyss/abyss-2.3.0.ebuild +++ b/sci-biology/abyss/abyss-2.3.0-r1.ebuild @@ -27,6 +27,10 @@ DEPEND="${RDEPEND} dev-lang/ghc )" +PATCHES=( "${FILESDIR}"/${PN}-2.2.5-PathConsensus-assert.patch + "${FILESDIR}"/${PN}-2.2.5-ContigProperties.h.patch + ) + # todo: --enable-maxk=N configure option # todo: fix automagic mpi toggling diff --git a/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch new file mode 100644 index 000000000..95181f082 --- /dev/null +++ b/sci-biology/abyss/files/abyss-2.2.5-ContigProperties.h.patch @@ -0,0 +1,11 @@ +--- abyss-2.2.5/Common/ContigProperties.h.ori 2020-09-18 20:42:12.000000000 +0200 ++++ abyss-2.2.5/Common/ContigProperties.h 2021-04-14 12:31:23.682158000 +0200 +@@ -171,7 +171,7 @@ + template <typename T> + ContigProperties& operator+=(ContigProperties& a, const T& b) + { +- assert((int)a.length + (int)b.distance > 0); ++ assert((int)a.length + (int)b.distance >= 0); + a.length += b.distance; + return a; + } diff --git a/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch new file mode 100644 index 000000000..754e25acc --- /dev/null +++ b/sci-biology/abyss/files/abyss-2.2.5-PathConsensus-assert.patch @@ -0,0 +1,11 @@ +--- abyss-2.2.5/MergePaths/PathConsensus.cpp 2020-09-18 20:42:12.000000000 +0200 ++++ abyss-2.2.5/MergePaths/PathConsensus.cpp 2021-04-12 22:26:28.780547000 +0200 +@@ -379,7 +379,7 @@ + unsigned overlap, Sequence& seq, + const Sequence& s, const ContigNode& node, const Path& path) + { +- assert(s.length() > overlap); ++ assert(s.length() >= overlap); + Sequence ao; + Sequence bo(s, 0, overlap); + Sequence o;
