diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology')
4 files changed, 5 insertions, 33 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix index febfde548fd7..006b46db9974 100644 --- a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix @@ -29,13 +29,13 @@ in stdenv.mkDerivation (finalAttrs: { pname = "dssp"; - version = "4.4.4.1"; + version = "4.4.5"; src = fetchFromGitHub { owner = "PDB-REDO"; repo = "dssp"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-sy6GBCnTGRD1YP00dKIolkr1RMboLGcd0f4kU8gCOnA="; + hash = "sha256-X0aMWqoMhmQVRHWKVm2S6JAOYiBuBBMzMoivMdpNx0M="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/igv/default.nix b/nixpkgs/pkgs/applications/science/biology/igv/default.nix index 52d388ab023d..a74208c706a1 100644 --- a/nixpkgs/pkgs/applications/science/biology/igv/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/igv/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchzip, jdk11 }: +{ lib, stdenv, fetchzip, jdk11, wrapGAppsHook }: stdenv.mkDerivation rec { pname = "igv"; @@ -24,6 +24,7 @@ stdenv.mkDerivation rec { chmod +x $out/bin/igv chmod +x $out/bin/igvtools ''; + nativeBuildInputs = [ wrapGAppsHook ]; meta = with lib; { homepage = "https://www.broadinstitute.org/igv/"; diff --git a/nixpkgs/pkgs/applications/science/biology/kent/default.nix b/nixpkgs/pkgs/applications/science/biology/kent/default.nix index f1e891bb85aa..b6e4661ccfd6 100644 --- a/nixpkgs/pkgs/applications/science/biology/kent/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/kent/default.nix @@ -24,16 +24,12 @@ stdenv.mkDerivation rec { buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ]; - patchPhase = '' - runHook prePatch - + postPatch = '' substituteInPlace ./src/checkUmask.sh \ --replace "/bin/bash" "${bash}/bin/bash" substituteInPlace ./src/hg/sqlEnvTest.sh \ --replace "which mysql_config" "${which}/bin/which ${libmysqlclient}/bin/mysql_config" - - runHook postPatch ''; buildPhase = '' diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix deleted file mode 100644 index f2825eeb97be..000000000000 --- a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix +++ /dev/null @@ -1,25 +0,0 @@ -{ lib, nimPackages, fetchFromGitHub, docopt, hts, pcre }: - -nimPackages.buildNimPackage rec { - pname = "mosdepth"; - version = "0.3.5"; - nimBinOnly = true; - - src = fetchFromGitHub { - owner = "brentp"; - repo = "mosdepth"; - rev = "v${version}"; - sha256 = "sha256-tG3J51PS6A0WBCZ+j/Nf7aaukFV+DZJsxpbTbvwu0zc="; - }; - - buildInputs = [ docopt hts pcre ]; - nimFlags = hts.nimFlags ++ [ "--threads:off" ]; - - meta = with lib; { - description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing"; - license = licenses.mit; - homepage = "https://github.com/brentp/mosdepth"; - maintainers = with maintainers; [ jbedo ]; - platforms = platforms.linux; - }; -} |