Merge pull request #24840 from matthiasbeyer/pr-23111-fixed

diamond: init at 0.8.36
This commit is contained in:
Jörg Thalheim 2017-04-13 14:40:30 +02:00 committed by GitHub
commit 478e9cdae5
3 changed files with 63 additions and 0 deletions

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@ -0,0 +1,41 @@
{ stdenv, fetchurl, cmake, gcc, zlib }:
stdenv.mkDerivation rec {
name = "diamond-0.8.36";
src = fetchurl {
url = "https://github.com/bbuchfink/diamond/archive/v0.8.36.tar.gz";
sha256 = "092smzzjcg51n3x4h84k52ijpz9m40ri838j9k2i463ribc3c8rh";
};
patches = [
./diamond-0.8.36-no-warning.patch
];
nativeBuildInputs = [ cmake ];
buildInputs = [ zlib ];
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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@ -0,0 +1,20 @@
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_
+#include <cmath>
#include <exception>
#include "../basic/score_matrix.h"
@@ -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;
}
template<typename _score>

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@ -17200,6 +17200,8 @@ with pkgs;
bcftools = callPackage ../applications/science/biology/bcftools { };
diamond = callPackage ../applications/science/biology/diamond { };
ecopcr = callPackage ../applications/science/biology/ecopcr { };
emboss = callPackage ../applications/science/biology/emboss { };