diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology')
10 files changed, 86 insertions, 40 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/bioawk/default.nix b/nixpkgs/pkgs/applications/science/biology/bioawk/default.nix new file mode 100644 index 000000000000..cfbb1a551fac --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/bioawk/default.nix @@ -0,0 +1,50 @@ +{ lib +, stdenv +, fetchFromGitHub +, installShellFiles +, bison +, zlib +}: + +stdenv.mkDerivation { + pname = "bioawk"; + version = "unstable-2017-09-11"; + + src = fetchFromGitHub { + owner = "lh3"; + repo = "bioawk"; + rev = "fd40150b7c557da45e781a999d372abbc634cc21"; + hash = "sha256-WWgz96DPP83J45isWkMbgEvOlibq6WefK//ImV6+AU0="; + }; + + nativeBuildInputs = [ + bison + installShellFiles + ]; + + buildInputs = [ + zlib + ]; + + buildFlags = [ + "CC=${stdenv.cc.targetPrefix}cc" + ]; + + installPhase = '' + runHook preInstall + + install -Dm755 bioawk -t $out/bin + mv awk.1 bioawk.1 + installManPage bioawk.1 + + runHook postInstall + ''; + + meta = with lib; { + description = "BWK awk modified for biological data"; + homepage = "https://github.com/lh3/bioawk"; + license = licenses.hpnd; + maintainers = with maintainers; [ natsukium ]; + platforms = platforms.unix; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/blast/bin.nix b/nixpkgs/pkgs/applications/science/biology/blast/bin.nix index daae9c096144..48537a568e4b 100644 --- a/nixpkgs/pkgs/applications/science/biology/blast/bin.nix +++ b/nixpkgs/pkgs/applications/science/biology/blast/bin.nix @@ -13,20 +13,20 @@ }: let pname = "blast-bin"; - version = "2.13.0"; + version = "2.14.1"; srcs = rec { x86_64-linux = fetchurl { url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-x64-linux.tar.gz"; - hash = "sha256-QPK3OdT++GoNI1NHyEpu2/hB2hqHYPQ/vNXFAVCwVEc="; + hash = "sha256-OO8MNOk6k0J9FlAGyCOhP+hirEIT6lL+rIInB8dQWEU="; }; aarch64-linux = fetchurl { - url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-x64-arm-linux.tar.gz"; - hash = "sha256-vY8K66k7KunpBUjFsJTTb+ur5n1XmU0/mYxhZsi9ycs="; + url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-aarch64-linux.tar.gz"; + hash = "sha256-JlOyoxZQBbvUcHIMv5muTuGQgrh2uom3rzDurhHQ+FM="; }; x86_64-darwin = fetchurl { url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-x64-macosx.tar.gz"; - hash = "sha256-Y0JlOUl9Ego6LTxTCNny3P5c1H3fApPXQm7Z6Zhq9RA="; + hash = "sha256-eMfuwMCD6VlDgeshLslDhYBBp0YOpL+6q/zSchR0bAs="; }; aarch64-darwin = x86_64-darwin; }; @@ -55,6 +55,7 @@ stdenv.mkDerivation { meta = with lib; { inherit (blast.meta) description homepage license; platforms = [ "x86_64-linux" "aarch64-linux" "x86_64-darwin" "aarch64-darwin" ]; + sourceProvenance = with sourceTypes; [ binaryNativeCode ]; maintainers = with maintainers; [ natsukium ]; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix index 954b704be0c6..e5c9c2864225 100644 --- a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "bowtie2"; - version = "2.5.1"; + version = "2.5.2"; src = fetchFromGitHub { owner = "BenLangmead"; repo = pname; rev = "v${version}"; - sha256 = "sha256-HaiZmWU6akHXJVWBmCvkG2E61NDrAP7UIxx9DNCEZqE="; + sha256 = "sha256-Bem4SHY/74suZPDbw/rwKMLBn3bRq5ooHbBoVnKuYk0="; }; nativeBuildInputs = [ cmake ]; diff --git a/nixpkgs/pkgs/applications/science/biology/delly/default.nix b/nixpkgs/pkgs/applications/science/biology/delly/default.nix index 92eda1d1dd13..1c39d209c34e 100644 --- a/nixpkgs/pkgs/applications/science/biology/delly/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/delly/default.nix @@ -13,13 +13,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "delly"; - version = "1.1.6"; + version = "1.1.7"; src = fetchFromGitHub { owner = "dellytools"; repo = "delly"; rev = "v${finalAttrs.version}"; - hash = "sha256-/I//7MhsC/CcBeIJblzbjXp/yOSBm83KWJsrYpl6UJk="; + hash = "sha256-oBIY8s/ippf+Xw+3QzMwP0Esc/QpiT6yWeAnqpMix6s="; }; buildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix index 1281643fe794..78f226350f60 100644 --- a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix @@ -1,6 +1,7 @@ { lib , stdenv , cmake +, eigen , fetchFromGitHub , libcifpp , libmcfp @@ -8,24 +9,24 @@ }: let libcifpp' = libcifpp.overrideAttrs (oldAttrs: { - # dssp 4.3.1 requires specific version "5.1.0" of libcifpp - version = "5.1.0"; + # dssp 4.4.3 requires specific version "5.2.0" of libcifpp + version = "5.2.0"; src = fetchFromGitHub { inherit (oldAttrs.src) owner repo rev; - hash = "sha256-PUsi4T6huSqwaa6RnBP1Vj+0a1ePrvrHD0641Lkkc5s="; + hash = "sha256-Sj10j6HxUoUvQ66cd2B8CO7CVBRd7w9CTovxkwPDOvs="; }; }); in stdenv.mkDerivation (finalAttrs: { pname = "dssp"; - version = "4.4.2"; + version = "4.4.3"; src = fetchFromGitHub { owner = "PDB-REDO"; repo = "dssp"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-Gic/rE/G24P5g4Uhf2lcvVa6i/4KGQzCpK4KlpjXcS0="; + hash = "sha256-zPmRR7sxVNErwabLqA5CNMO4K1qHdmC9FBPjcx91KuM="; }; nativeBuildInputs = [ @@ -33,6 +34,7 @@ stdenv.mkDerivation (finalAttrs: { ]; buildInputs = [ + eigen libcifpp' libmcfp zlib diff --git a/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix b/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix index 2a4df9d21dba..243e067ddec3 100644 --- a/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix @@ -1,12 +1,12 @@ { lib, stdenv, fetchurl }: stdenv.mkDerivation rec { - version = "3.3.2"; + version = "3.4"; pname = "hmmer"; src = fetchurl { url = "http://eddylab.org/software/hmmer/${pname}-${version}.tar.gz"; - sha256 = "0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj"; + sha256 = "sha256-ynDZT9DPJxvXBjQjqrsRbULeUzEXNDqbJ6ZcF/8G+/M="; }; meta = with lib; { @@ -18,6 +18,7 @@ stdenv.mkDerivation rec { HMMER can be downloaded and installed as a command line tool on your own hardware, and now it is also more widely accessible to the scientific community via new search servers at the European Bioinformatics Institute. ''; homepage = "http://hmmer.org/"; + changelog = "https://github.com/EddyRivasLab/hmmer/blob/hmmer-${version}/release-notes/RELEASE-${version}.md"; license = licenses.gpl3; maintainers = [ maintainers.iimog ]; # at least SSE is *required* diff --git a/nixpkgs/pkgs/applications/science/biology/nest/default.nix b/nixpkgs/pkgs/applications/science/biology/nest/default.nix index 90fa69812473..5f0ad540f696 100644 --- a/nixpkgs/pkgs/applications/science/biology/nest/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/nest/default.nix @@ -20,13 +20,13 @@ stdenv.mkDerivation rec { pname = "nest"; - version = "3.5"; + version = "3.6"; src = fetchFromGitHub { owner = "nest"; repo = "nest-simulator"; rev = "v${version}"; - hash = "sha256-PPUIXlU6noJRAa/twNSKVxPgIvbWl0OillEJRDzt+4s="; + hash = "sha256-sXtF4JmHYoLp0t3o4KF6R2E0qLnKrzSPMXOxVJAm+sU="; }; postPatch = '' diff --git a/nixpkgs/pkgs/applications/science/biology/neuron/default.nix b/nixpkgs/pkgs/applications/science/biology/neuron/default.nix index 5b08fbfd6704..6e5e4feb16fc 100644 --- a/nixpkgs/pkgs/applications/science/biology/neuron/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/neuron/default.nix @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { pname = "neuron"; - version = "8.2.2"; + version = "8.2.3"; # format is for pythonModule conversion format = "other"; @@ -83,7 +83,7 @@ stdenv.mkDerivation rec { src = fetchurl { url = "https://github.com/neuronsimulator/nrn/releases/download/${version}/full-src-package-${version}.tar.gz"; - sha256 = "sha256-orGeBxu3pu4AyAW5P1EGJv8G0dOUZcSOjpUaloqicZU="; + sha256 = "sha256-k8+71BRfh+a73sZho6v0QFRxVmrfx6jqrgaqammdtDI="; }; meta = with lib; { diff --git a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix index 04ef7c2e062b..0a18c5f40fda 100644 --- a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "stacks"; - version = "2.62"; + version = "2.65"; src = fetchurl { url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz"; - sha256 = "sha256-7uhQVLC/AEPAPUdm3+vABoIwG4uhNy/EngjsrZjT0Ts="; + sha256 = "sha256-/9a9PWKVq5yJzEUfOF03zR1Hp3AZw9MF8xICoriV4uo="; }; buildInputs = [ zlib ]; @@ -15,5 +15,6 @@ stdenv.mkDerivation rec { homepage = "http://catchenlab.life.illinois.edu/stacks/"; maintainers = [ lib.maintainers.bzizou ]; license = lib.licenses.gpl3Plus; + platforms = lib.platforms.linux; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/truvari/default.nix b/nixpkgs/pkgs/applications/science/biology/truvari/default.nix index e626af56278f..946f4be60632 100644 --- a/nixpkgs/pkgs/applications/science/biology/truvari/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/truvari/default.nix @@ -1,6 +1,5 @@ { lib , fetchFromGitHub -, fetchpatch , python3Packages , runtimeShell , bcftools @@ -16,37 +15,28 @@ let }; in python3Packages.buildPythonApplication rec { pname = "truvari"; - version = "4.0.0"; + version = "4.1.0"; + pyproject = true; src = fetchFromGitHub { owner = "ACEnglish"; repo = "truvari"; rev = "v${version}"; - hash = "sha256-UJNMKEV5m2jFqnWvkVAtymkcE2TjPIXp7JqRZpMSqsE="; + hash = "sha256-HFVAv1TTL/nMjr62tQKhMdwh25P/y4nBGzSbxoJxMmo="; }; - patches = [ - (fetchpatch { - name = "fix-anno-trf-on-darwin.patch"; - url = "https://github.com/ACEnglish/truvari/commit/f9f36305e8eaa88f951562210e3672a4d4f71265.patch"; - hash = "sha256-7O9jTQDCC2b8hUBm0qJQCYMzTC9NFtn/E0dTHSfJALU="; - }) - (fetchpatch { - name = "fix-anno-grm-on-darwin.patch"; - url = "https://github.com/ACEnglish/truvari/commit/31416552008a506204ed4e2add55474f10392357.patch"; - hash = "sha256-42u0ewZU38GCoSfff+XQFv9hEFeO3WlJufTHcl6vkN4="; - }) - ]; - postPatch = '' - substituteInPlace setup.py \ - --replace "rich==" "rich>=" substituteInPlace truvari/utils.py \ --replace "/bin/bash" "${runtimeShell}" patchShebangs repo_utils/test_files ''; + nativeBuildInputs = [ + python3Packages.setuptools + ]; + propagatedBuildInputs = with python3Packages; [ + pywfa rich edlib pysam @@ -83,6 +73,7 @@ in python3Packages.buildPythonApplication rec { meta = with lib; { description = "Structural variant comparison tool for VCFs"; homepage = "https://github.com/ACEnglish/truvari"; + changelog = "https://github.com/ACEnglish/truvari/releases/tag/${src.rev}"; license = licenses.mit; maintainers = with maintainers; [ natsukium scalavision ]; longDescription = '' |