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Merge pull request #24840 from matthiasbeyer/pr-23111-fixed
diamond: init at 0.8.36
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{ stdenv, fetchurl, cmake, gcc, zlib }: | ||
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stdenv.mkDerivation rec { | ||
name = "diamond-0.8.36"; | ||
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src = fetchurl { | ||
url = "https://github.com/bbuchfink/diamond/archive/v0.8.36.tar.gz"; | ||
sha256 = "092smzzjcg51n3x4h84k52ijpz9m40ri838j9k2i463ribc3c8rh"; | ||
}; | ||
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patches = [ | ||
./diamond-0.8.36-no-warning.patch | ||
]; | ||
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nativeBuildInputs = [ cmake ]; | ||
buildInputs = [ zlib ]; | ||
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meta = with stdenv.lib; { | ||
description = "Accelerated BLAST compatible local sequence aligner"; | ||
longDescription = '' | ||
A sequence aligner for protein and translated DNA | ||
searches and functions as a drop-in replacement for the NCBI BLAST | ||
software tools. It is suitable for protein-protein search as well as | ||
DNA-protein search on short reads and longer sequences including contigs | ||
and assemblies, providing a speedup of BLAST ranging up to x20,000. | ||
DIAMOND is developed by Benjamin Buchfink. Feel free to contact him for support (Email Twitter). | ||
If you use DIAMOND in published research, please cite | ||
B. Buchfink, Xie C., D. Huson, | ||
"Fast and sensitive protein alignment using DIAMOND", | ||
Nature Methods 12, 59-60 (2015). | ||
''; | ||
homepage = https://github.com/bbuchfink/diamond; | ||
license = { | ||
fullName = "University of Tuebingen, Benjamin Buchfink"; | ||
url = https://raw.githubusercontent.com/bbuchfink/diamond/master/src/COPYING; | ||
}; | ||
maintainers = [ maintainers.metabar ]; | ||
}; | ||
} |
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pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch
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diff -u -r diamond-0.8.36/src/dp/scalar_traceback.h diamond-0.8.36-patched/src/dp/scalar_traceback.h | ||
--- diamond-0.8.36/src/dp/scalar_traceback.h 2017-02-06 16:32:05.000000000 +0100 | ||
+++ diamond-0.8.36-patched/src/dp/scalar_traceback.h 2017-02-23 15:13:24.000000000 +0100 | ||
@@ -19,6 +19,7 @@ | ||
#ifndef SCALAR_TRACEBACK_H_ | ||
#define SCALAR_TRACEBACK_H_ | ||
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+#include <cmath> | ||
#include <exception> | ||
#include "../basic/score_matrix.h" | ||
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@@ -31,7 +32,7 @@ | ||
template<> | ||
inline bool almost_equal<float>(float x, float y) | ||
{ | ||
- return abs(x - y) < 0.001f; | ||
+ return std::abs(x - y) < 0.001f; | ||
} | ||
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template<typename _score> |
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