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author | Matthias Beyer <mail@beyermatthias.de> | 2017-04-12 13:05:22 +0200 |
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committer | Matthias Beyer <mail@beyermatthias.de> | 2017-04-12 13:05:57 +0200 |
commit | 6239da6ade413ce89503d608c9b827ac17359e64 (patch) | |
tree | a90e404a3b80c5d4161c5ae124ef4d54e5eedb57 /pkgs/applications/science/biology | |
parent | ffa2bc2382a82994755c60f8bab1193dc62fd3fa (diff) | |
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diamond: init at 0.8.36
Diffstat (limited to 'pkgs/applications/science/biology')
-rw-r--r-- | pkgs/applications/science/biology/diamond/default.nix | 41 | ||||
-rw-r--r-- | pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch | 20 |
2 files changed, 61 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/diamond/default.nix b/pkgs/applications/science/biology/diamond/default.nix new file mode 100644 index 00000000000..a45e5df2f52 --- /dev/null +++ b/pkgs/applications/science/biology/diamond/default.nix @@ -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 ]; + }; +} diff --git a/pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch b/pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch new file mode 100644 index 00000000000..a16d475c556 --- /dev/null +++ b/pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch @@ -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> |