diff options
author | scalavision <scalavison@gmail.com> | 2019-10-30 21:29:37 +0100 |
---|---|---|
committer | Lassulus <github@lassul.us> | 2019-12-08 14:51:05 +0100 |
commit | 3dfabd6eff612582b34b4ab9777dbea32cc003f7 (patch) | |
tree | d9b4a1f5466dfe42659687525e513649b4372ea5 /pkgs | |
parent | 24c1f9505a06b2e81a87b21ef4ba5f3073ed214a (diff) |
svaba: init at 1.1.0
Diffstat (limited to 'pkgs')
-rw-r--r-- | pkgs/applications/science/biology/svaba/default.nix | 42 | ||||
-rw-r--r-- | pkgs/top-level/all-packages.nix | 2 |
2 files changed, 44 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/svaba/default.nix b/pkgs/applications/science/biology/svaba/default.nix new file mode 100644 index 0000000000000..ae8dc95d6fea2 --- /dev/null +++ b/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. + ''; + + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index c70b9212856ce..1219d52cbb66d 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -23687,6 +23687,8 @@ in SPAdes = callPackage ../applications/science/biology/spades { }; + svaba = callPackage ../applications/science/biology/svaba { }; + trimal = callPackage ../applications/science/biology/trimal { }; truvari = callPackage ../applications/science/biology/truvari { }; |