49 lines
1.9 KiB
Nix
49 lines
1.9 KiB
Nix
{ lib, stdenv, zlib, bzip2, xz, fetchFromGitHub } :
|
|
|
|
stdenv.mkDerivation rec {
|
|
version = "1.1.0";
|
|
pname = "svaba";
|
|
|
|
src = fetchFromGitHub {
|
|
owner = "walaj";
|
|
repo = pname;
|
|
rev = version;
|
|
sha256 = "1vv5mc9z5d22kgdy7mm27ya5aahnqgkcrskdr2405058ikk9g8kp";
|
|
fetchSubmodules = true;
|
|
};
|
|
|
|
buildInputs = [ zlib bzip2 xz ];
|
|
|
|
# Workaround build failure on -fno-common toolchains like upstream
|
|
# gcc-10. Otherwise build fails as:
|
|
# ld: ./libfml.a(rle.o):/build/source/SeqLib/fermi-lite/rle.h:33: multiple definition of
|
|
# `rle_auxtab'; ./libfml.a(misc.o):/build/source/SeqLib/fermi-lite/rle.h:33: first defined here
|
|
env.NIX_CFLAGS_COMPILE = "-fcommon";
|
|
|
|
installPhase = ''
|
|
runHook preInstall
|
|
install -Dm555 src/svaba/svaba $out/bin/svaba
|
|
runHook postInstall
|
|
'';
|
|
|
|
meta = with lib; {
|
|
broken = (stdenv.isLinux && stdenv.isAarch64);
|
|
description = "Structural variant and INDEL caller for DNA sequencing data, using genome-wide local assembly";
|
|
license = licenses.gpl3;
|
|
homepage = "https://github.com/walaj/svaba";
|
|
maintainers = with maintainers; [ scalavision ];
|
|
platforms = platforms.linux;
|
|
longDescription = ''
|
|
SvABA is a method for detecting structural variants in sequencing data
|
|
using genome-wide local assembly. Under the hood, SvABA uses a custom
|
|
implementation of SGA (String Graph Assembler) by Jared Simpson,
|
|
and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window
|
|
(with some small overlap) for every region in the genome.
|
|
The default is to use only clipped, discordant, unmapped and indel reads,
|
|
although this can be customized to any set of reads at the command line using VariantBam rules.
|
|
These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants.
|
|
Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support.
|
|
'';
|
|
|
|
};
|
|
}
|