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RAxML: init at 8.2.11 (SSE3 & MPI)

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This can potentially be extended to cover all the other compilation
targets. SSE3-PTHREADS and MPI being the most commonly used.
This commit is contained in:
Renato Alves 2018-02-02 02:24:19 +01:00
parent 9a5fe79d07
commit 05889c52b9
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GPG key ID: A703C12A2FA65D04
2 changed files with 48 additions and 0 deletions
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42
pkgs/applications/science/biology/raxml/default.nix Normal file
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@ -0,0 +1,42 @@
{ stdenv
, fetchFromGitHub
, zlib
, pkgs
, mpi ? false
}:
stdenv.mkDerivation rec {
pname = "RAxML";
version = "8.2.11";
name = "${pname}-${version}";
src = fetchFromGitHub {
owner = "stamatak";
repo = "standard-${pname}";
rev = "v${version}";
sha256 = "08fmqrr7y5a2fmmrgfz2p0hmn4mn71l5yspxfcwwsqbw6vmdfkhg";
};
buildInputs = if mpi then [ pkgs.openmpi ] else [];
# TODO darwin, AVX and AVX2 makefile targets
buildPhase = if mpi then ''
make -f Makefile.MPI.gcc
'' else ''
make -f Makefile.SSE3.PTHREADS.gcc
'';
installPhase = if mpi then ''
mkdir -p $out/bin && cp raxmlHPC-MPI $out/bin
'' else ''
mkdir -p $out/bin && cp raxmlHPC-PTHREADS-SSE3 $out/bin
'';
meta = with stdenv.lib; {
description = "A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies";
license = licenses.gpl3;
homepage = https://sco.h-its.org/exelixis/web/software/raxml/;
maintainers = [ maintainers.unode ];
platforms = [ "i686-linux" "x86_64-linux" ];
};
}

6
pkgs/top-level/all-packages.nix
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@ -19044,6 +19044,12 @@ with pkgs;
plink-ng = callPackage ../applications/science/biology/plink-ng/default.nix { };
raxml = callPackage ../applications/science/biology/raxml { };
raxml-mpi = appendToName "mpi" (raxml.override {
mpi = true;
});
samtools = callPackage ../applications/science/biology/samtools/default.nix { };
snpeff = callPackage ../applications/science/biology/snpeff/default.nix { };