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author | Alyssa Ross <hi@alyssa.is> | 2020-01-11 23:37:02 +0000 |
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committer | Alyssa Ross <hi@alyssa.is> | 2020-01-11 23:41:30 +0000 |
commit | 6c557e3f1c28cf87e9fba232811d6875dd1399c1 (patch) | |
tree | 035a071d5d8980df6de0fa42e2ef8fc0cce7055e /nixpkgs/pkgs/applications/science/biology/svaba/default.nix | |
parent | da7500bc026e937ac7fce7b50f67a0e1765737a7 (diff) | |
parent | e4134747f5666bcab8680aff67fa3b63384f9a0f (diff) | |
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Merge commit 'e4134747f5666bcab8680aff67fa3b63384f9a0f'
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology/svaba/default.nix')
-rw-r--r-- | nixpkgs/pkgs/applications/science/biology/svaba/default.nix | 42 |
1 files changed, 42 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/svaba/default.nix b/nixpkgs/pkgs/applications/science/biology/svaba/default.nix new file mode 100644 index 000000000000..ae8dc95d6fea --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/svaba/default.nix @@ -0,0 +1,42 @@ +{ stdenv, zlib, bzip2, lzma, 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 lzma ]; + + installPhase = '' + runHook preInstall + install -Dm555 src/svaba/svaba $out/bin/svaba + runHook postInstall + ''; + + meta = with stdenv.lib; { + 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. + ''; + + }; +} |