diff options
Diffstat (limited to 'pkgs/applications/science/biology')
5 files changed, 67 insertions, 26 deletions
diff --git a/pkgs/applications/science/biology/blast/bin.nix b/pkgs/applications/science/biology/blast/bin.nix index 03e61bdcbe867..daae9c096144a 100644 --- a/pkgs/applications/science/biology/blast/bin.nix +++ b/pkgs/applications/science/biology/blast/bin.nix @@ -35,7 +35,7 @@ in stdenv.mkDerivation { inherit pname version src; - nativeBuildInputs = lib.optional stdenv.isLinux [ autoPatchelfHook ]; + nativeBuildInputs = lib.optionals stdenv.isLinux [ autoPatchelfHook ]; buildInputs = [ python3 perl ] ++ lib.optionals stdenv.isLinux [ zlib bzip2 glib libxml2 ]; diff --git a/pkgs/applications/science/biology/dssp/default.nix b/pkgs/applications/science/biology/dssp/default.nix index 762b0515e85c2..59da360d1b6df 100644 --- a/pkgs/applications/science/biology/dssp/default.nix +++ b/pkgs/applications/science/biology/dssp/default.nix @@ -1,19 +1,30 @@ -{ lib, stdenv, fetchFromGitHub, boost, cmake, libcifpp, zlib, }: +{ lib, stdenv, fetchFromGitHub, cmake, libcifpp, libmcfp, zlib }: +let + libcifpp' = libcifpp.overrideAttrs (oldAttrs: rec { + # dssp 4.2.2.1 requires specific version "5.0.8" of libcifpp + version = "5.0.8"; + src = fetchFromGitHub { + inherit (oldAttrs.src) owner repo; + rev = "v${version}"; + sha256 = "sha256-KJGcopGhCWSl+ElG3BPJjBf/kvYJowOHxto6Ci1IMco="; + }; + }); +in stdenv.mkDerivation rec { pname = "dssp"; - version = "4.0.5"; + version = "4.2.2.1"; src = fetchFromGitHub { owner = "PDB-REDO"; repo = pname; rev = "v${version}"; - sha256 = "1x35rdcm4fch66pjbmy73lv0gdb6g9y3v023a66512a6nzsqjsir"; + sha256 = "sha256-vmGvC5d8LTo+pcY9sxwj0d6JvH8Lyk+QSOZo5raBci4="; }; nativeBuildInputs = [ cmake ]; - buildInputs = [ boost libcifpp zlib ]; + buildInputs = [ libcifpp' libmcfp zlib ]; meta = with lib; { description = "Calculate the most likely secondary structure assignment given the 3D structure of a protein"; diff --git a/pkgs/applications/science/biology/subread/default.nix b/pkgs/applications/science/biology/subread/default.nix index d083e202a9ffe..45f0a1d7f4626 100644 --- a/pkgs/applications/science/biology/subread/default.nix +++ b/pkgs/applications/science/biology/subread/default.nix @@ -6,11 +6,11 @@ stdenv.mkDerivation rec { pname = "subread"; - version = "2.0.4"; + version = "2.0.5"; src = fetchurl { url = "mirror://sourceforge/subread/subread-${version}/subread-${version}-source.tar.gz"; - sha256 = "sha256-xUs37YOzQxjY8Rm1wC+50KZcgRGVvMnhdF322vdMots="; + sha256 = "sha256-frZzd+IV4IxfPK44PWOgV9yPRPoUB3smPbxoDchbaSc="; }; buildInputs = [ diff --git a/pkgs/applications/science/biology/tandem-aligner/default.nix b/pkgs/applications/science/biology/tandem-aligner/default.nix index 53daffbe0677e..5f197bd7f79cd 100644 --- a/pkgs/applications/science/biology/tandem-aligner/default.nix +++ b/pkgs/applications/science/biology/tandem-aligner/default.nix @@ -6,14 +6,14 @@ , zlib }: -stdenv.mkDerivation { +stdenv.mkDerivation (finalAttrs: { pname = "TandemAligner"; - version = "unstable-2022-09-17"; + version = "0.1"; src = fetchFromGitHub { owner = "seryrzu"; repo = "tandem_aligner"; - rev = "ac6004f108ad20477045f4d0b037d96051a9df70"; + rev = "v${finalAttrs.version}"; hash = "sha256-iMDj1HZ8LzmZckuAM3lbG3eSJSd/5JGVA6SBs7+AgX8="; }; @@ -58,9 +58,10 @@ stdenv.mkDerivation { meta = { description = "A parameter-free algorithm for sequence alignment"; homepage = "https://github.com/seryrzu/tandem_aligner"; + changelog = "https://github.com/seryrzu/tandem_aligner/releases/tag/v${finalAttrs.version}"; license = lib.licenses.bsd3; maintainers = with lib.maintainers; [ amesgen ]; platforms = lib.platforms.linux; mainProgram = "tandem_aligner"; }; -} +}) diff --git a/pkgs/applications/science/biology/truvari/default.nix b/pkgs/applications/science/biology/truvari/default.nix index 412642f523f2d..cf64070d782f2 100644 --- a/pkgs/applications/science/biology/truvari/default.nix +++ b/pkgs/applications/science/biology/truvari/default.nix @@ -1,47 +1,76 @@ { lib , fetchFromGitHub , python3Packages +, runtimeShell +, bcftools +, htslib }: -python3Packages.buildPythonApplication rec { +let + ssshtest = fetchFromGitHub { + owner = "ryanlayer"; + repo = "ssshtest"; + rev = "d21f7f928a167fca6e2eb31616673444d15e6fd0"; + hash = "sha256-zecZHEnfhDtT44VMbHLHOhRtNsIMWeaBASupVXtmrks="; + }; +in python3Packages.buildPythonApplication rec { pname = "truvari"; - version = "2.1.1"; + version = "4.0.0"; src = fetchFromGitHub { - owner = "spiralgenetics"; + owner = "ACEnglish"; repo = "truvari"; rev = "v${version}"; - sha256 = "14nsdbj063qm175xxixs34cihvsiskc9gym8pg7gbwsh13k5a00h"; + hash = "sha256-UJNMKEV5m2jFqnWvkVAtymkcE2TjPIXp7JqRZpMSqsE="; }; postPatch = '' substituteInPlace setup.py \ - --replace 'python-Levenshtein==0.12.1' 'python-Levenshtein>=0.12.1' + --replace "rich==" "rich>=" + substituteInPlace truvari/utils.py \ + --replace "/bin/bash" "${runtimeShell}" + patchShebangs repo_utils/test_files ''; propagatedBuildInputs = with python3Packages; [ - pyvcf - levenshtein - progressbar2 + rich + edlib pysam - pyfaidx intervaltree + joblib + numpy pytabix - acebinf bwapy - joblib pandas ]; - # no tests - doCheck = false; + makeWrapperArgs = [ + "--prefix" "PATH" ":" (lib.makeBinPath [ bcftools htslib ]) + ]; + pythonImportsCheck = [ "truvari" ]; + nativeCheckInputs = [ + bcftools + htslib + ] ++ (with python3Packages; [ + coverage + ]); + + checkPhase = '' + runHook preCheck + + ln -s ${ssshtest}/ssshtest . + bash repo_utils/truvari_ssshtests.sh + + runHook postCheck + ''; + meta = with lib; { description = "Structural variant comparison tool for VCFs"; - homepage = "https://github.com/spiralgenetics/truvari"; + homepage = "https://github.com/ACEnglish/truvari"; license = licenses.mit; - maintainers = with maintainers; [ scalavision ]; + maintainers = with maintainers; [ natsukium scalavision ]; longDescription = '' Truvari is a benchmarking tool for comparison sets of SVs. It can calculate the recall, precision, and f-measure of a |