diff options
Diffstat (limited to 'pkgs/applications/science/biology')
18 files changed, 76 insertions, 98 deletions
diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix index 818d0fe14ba25..1702079e017fe 100644 --- a/pkgs/applications/science/biology/bowtie2/default.nix +++ b/pkgs/applications/science/biology/bowtie2/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "bowtie2"; - version = "2.4.4"; + version = "2.4.5"; src = fetchFromGitHub { owner = "BenLangmead"; repo = pname; rev = "v${version}"; - sha256 = "sha256-2B6w6c/qztyBb1jNA0zg+udQm41ouT1DyB6Ygpi5nC8="; + sha256 = "sha256-xCsTkQXrZS+Njn0YfidhPln+OwVfTXOqbtB0dCfTP2U="; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/biology/deeptools/default.nix b/pkgs/applications/science/biology/deeptools/default.nix index 2621c5bbf037f..1739a4c999a44 100644 --- a/pkgs/applications/science/biology/deeptools/default.nix +++ b/pkgs/applications/science/biology/deeptools/default.nix @@ -2,13 +2,13 @@ with python.pkgs; buildPythonApplication rec { pname = "deepTools"; - version = "3.5.0"; + version = "3.5.1"; src = fetchFromGitHub { owner = "deeptools"; repo = "deepTools"; rev = version; - sha256 = "1bz8ln32mfc9k8l9wgp034vw80dxh6f92dfqxhcrpggk4akwj6ml"; + sha256 = "07v8vb2x4b0mgw0mvcj91vj1fqbcwizwsniysl2cvmv93gad8gbp"; }; propagatedBuildInputs = [ diff --git a/pkgs/applications/science/biology/hisat2/default.nix b/pkgs/applications/science/biology/hisat2/default.nix index ab8e26f92a0de..67c39031b773a 100644 --- a/pkgs/applications/science/biology/hisat2/default.nix +++ b/pkgs/applications/science/biology/hisat2/default.nix @@ -37,8 +37,8 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Graph based aligner"; - license = licenses.gpl3; - homepage = "https://ccb.jhu.edu/software/hisat2/index.shtml"; + license = licenses.gpl3Plus; + homepage = "https://daehwankimlab.github.io/hisat2/"; maintainers = with maintainers; [ jbedo ]; platforms = [ "x86_64-linux" "i686-linux" ]; }; diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix index 203d0520660f0..156f55161291c 100644 --- a/pkgs/applications/science/biology/kallisto/default.nix +++ b/pkgs/applications/science/biology/kallisto/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "kallisto"; - version = "0.46.2"; + version = "0.48.0"; src = fetchFromGitHub { repo = "kallisto"; owner = "pachterlab"; rev = "v${version}"; - sha256 = "0m0r2820ca3rch99md1zzbgkilmlfkhdkpys2lfnb87qxmf1jnmb"; + sha256 = "sha256-r0cdR0jTRa1wu/LDKW6NdxI3XaKj6wcIVbIlct0fFvI="; }; nativeBuildInputs = [ autoconf cmake ]; diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 8de0580a8199b..68cdd9f120bfc 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1256"; + version = "1260"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = version; - sha256 = "sha256-lOsU0X4K6jYcbkTzwQV+KAerQh9odE4zCLtSgZrYH6s="; + sha256 = "sha256-bJNvoHr2sQYtiC3tr1GA0T0kRhDyx6hU3OOSTvKUSCs="; }; nativeBuildInputs = [ unzip ]; diff --git a/pkgs/applications/science/biology/lumpy/default.nix b/pkgs/applications/science/biology/lumpy/default.nix deleted file mode 100644 index 91a001744474c..0000000000000 --- a/pkgs/applications/science/biology/lumpy/default.nix +++ /dev/null @@ -1,50 +0,0 @@ -{ lib, stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba -, samtools, hexdump, python2Packages, which }: - -let - python = - python2Packages.python.withPackages (pkgs: with pkgs; [ pysam numpy ]); - -in stdenv.mkDerivation rec { - pname = "lumpy"; - version = "0.3.1"; - - src = fetchFromGitHub { - owner = "arq5x"; - repo = "lumpy-sv"; - rev = "v${version}"; - sha256 = "0r71sg7qch8r6p6dw995znrqdj6q49hjdylhzbib2qmv8nvglhs9"; - fetchSubmodules = true; - }; - - nativeBuildInputs = [ which ]; - buildInputs = - [ htslib zlib curl openssl python samblaster sambamba samtools hexdump ]; - - preConfigure = '' - patchShebangs ./. - - # Use Nix htslib over bundled version - sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile - sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile - # Also make sure we use the includes from Nix's htslib - sed -i 's|../../lib/htslib/|${htslib}|' src/filter/Makefile - ''; - - # Upstream's makefile doesn't have an install target - installPhase = '' - mkdir -p $out - cp -r bin $out - cp -r scripts $out - sed -i 's|/build/source|'$out'|' $out/bin/lumpyexpress.config - ''; - - meta = with lib; { - description = "Probabilistic structural variant caller"; - homepage = "https://github.com/arq5x/lumpy-sv"; - maintainers = with maintainers; [ jbedo ]; - license = licenses.mit; - platforms = [ "x86_64-linux" ]; - }; - -} diff --git a/pkgs/applications/science/biology/messer-slim/default.nix b/pkgs/applications/science/biology/messer-slim/default.nix index f8ce14e4685e5..79cce7b9f744e 100644 --- a/pkgs/applications/science/biology/messer-slim/default.nix +++ b/pkgs/applications/science/biology/messer-slim/default.nix @@ -1,14 +1,14 @@ { lib, stdenv, fetchFromGitHub, cmake, gcc, gcc-unwrapped }: stdenv.mkDerivation rec { - version = "3.6"; + version = "3.7.1"; pname = "messer-slim"; src = fetchFromGitHub { owner = "MesserLab"; repo = "SLiM"; rev = "v${version}"; - sha256 = "sha256-TSbGUfr8YzTRYTkbMfM2+K04Z3h5W4jakw+V4axOKm8="; + sha256 = "sha256-3ox+9hzqI8s4gmEkQ3Xm1Ih639LBtcSJNNmJgbpWaoM="; }; nativeBuildInputs = [ cmake gcc gcc-unwrapped ]; diff --git a/pkgs/applications/science/biology/minimap2/default.nix b/pkgs/applications/science/biology/minimap2/default.nix index 062cdd56c7c44..bba8a02b76e39 100644 --- a/pkgs/applications/science/biology/minimap2/default.nix +++ b/pkgs/applications/science/biology/minimap2/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "minimap2"; - version = "2.23"; + version = "2.24"; src = fetchFromGitHub { repo = pname; owner = "lh3"; rev = "v${version}"; - sha256 = "sha256-oNVpSINcXO2eKzOCr/Fl8tSMguRxzmlDNu7hLZeopoQ="; + sha256 = "sha256-sEp7/Y5ifV9LTqrkhlkfykTJYMMuc+VtF7PvmIpBxUw="; }; buildInputs = [ zlib ]; @@ -25,6 +25,7 @@ stdenv.mkDerivation rec { homepage = "https://lh3.github.io/minimap2"; license = licenses.mit; platforms = platforms.all; + badPlatforms = platforms.aarch64; maintainers = [ maintainers.arcadio ]; }; } diff --git a/pkgs/applications/science/biology/mosdepth/default.nix b/pkgs/applications/science/biology/mosdepth/default.nix index b6cc5e4061536..fa93ab3fcdb08 100644 --- a/pkgs/applications/science/biology/mosdepth/default.nix +++ b/pkgs/applications/science/biology/mosdepth/default.nix @@ -2,14 +2,14 @@ nimPackages.buildNimPackage rec { pname = "mosdepth"; - version = "0.3.2"; + version = "0.3.3"; nimBinOnly = true; src = fetchFromGitHub { owner = "brentp"; repo = "mosdepth"; rev = "v${version}"; - sha256 = "sha256-uui4yC7ok+pvbXVKfBVsAarH40fnH4fnP8P4uzOqztQ="; + sha256 = "sha256-de3h3SXnXlqjuLT1L66jj/1AoiTuFc3PVJYjm7s8Fj8="; }; buildInputs = with nimPackages; [ docopt hts-nim pcre ]; diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index f6dcca3a2399e..33d581ffd018d 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.26.9"; + version = "2.26.10"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "sha256-5e60StDQil9SMR9G6Gs+OPWMjADn96fOpfHDlNoZSGc="; + sha256 = "sha256-hKBWRmzyMVXiEmsz/eYbVIUhezZdSJnBvcgv6ShPI5U="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/biology/poretools/default.nix b/pkgs/applications/science/biology/poretools/default.nix index b2cefefb5cb55..efbedf9a121a0 100755 --- a/pkgs/applications/science/biology/poretools/default.nix +++ b/pkgs/applications/science/biology/poretools/default.nix @@ -1,6 +1,6 @@ -{ lib, pythonPackages, fetchFromGitHub }: +{ lib, python2Packages, fetchFromGitHub }: -pythonPackages.buildPythonPackage rec { +python2Packages.buildPythonPackage rec { pname = "poretools"; version = "unstable-2016-07-10"; @@ -11,7 +11,7 @@ pythonPackages.buildPythonPackage rec { sha256 = "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am"; }; - propagatedBuildInputs = [pythonPackages.h5py pythonPackages.matplotlib pythonPackages.seaborn pythonPackages.pandas]; + propagatedBuildInputs = [python2Packages.h5py python2Packages.matplotlib python2Packages.seaborn python2Packages.pandas]; meta = { description = "a toolkit for working with nanopore sequencing data from Oxford Nanopore"; diff --git a/pkgs/applications/science/biology/repseek/default.nix b/pkgs/applications/science/biology/repseek/default.nix new file mode 100644 index 0000000000000..5966c83b7a5fc --- /dev/null +++ b/pkgs/applications/science/biology/repseek/default.nix @@ -0,0 +1,27 @@ +{ lib, stdenv, fetchurl }: + +stdenv.mkDerivation rec { + pname = "repseek"; + version = "9Sep2014"; + src = fetchurl { + url = "https://bioinfo.mnhn.fr/abi/public/RepSeek/RepSeek.${version}.tgz"; + sha256 = "1jiknji3ivrv7zmrfbf2mccfpdwhin3lfxfsciaqwf69b3sda8nf"; + }; + + preConfigure = '' + mkdir -p $out/bin + substituteInPlace Makefile \ + --replace "INSTALLDIR = \$\$HOME/bin" "INSTALLDIR = $out/bin/" \ + --replace "CC= gcc" "CC = $CC" + '' + lib.optionalString stdenv.isLinux '' + substituteInPlace Makefile --replace "MACHINE = MACOSX" "MACHINE = LINUX" + ''; + + meta = { + description = "Tool to retrieve approximate repeats from large DNA sequences"; + homepage = "https://bioinfo.mnhn.fr/abi/public/RepSeek"; + maintainers = [ lib.maintainers.bzizou ]; + license = lib.licenses.lgpl21; + }; + +} diff --git a/pkgs/applications/science/biology/sambamba/default.nix b/pkgs/applications/science/biology/sambamba/default.nix index 03ee40013c778..36e950a181212 100644 --- a/pkgs/applications/science/biology/sambamba/default.nix +++ b/pkgs/applications/science/biology/sambamba/default.nix @@ -1,27 +1,27 @@ -{ lib, stdenv, fetchFromGitHub, fetchpatch, python3, which, ldc, zlib }: +{ lib +, stdenv +, fetchFromGitHub +, python3 +, which +, ldc +, zlib +, lz4 +}: stdenv.mkDerivation rec { pname = "sambamba"; - version = "0.8.1"; + version = "0.8.2"; src = fetchFromGitHub { owner = "biod"; repo = "sambamba"; rev = "v${version}"; - sha256 = "0f4qngnys2zjb0ri54k6kxqnssg938mnnscs4z9713hjn41rk7yd"; + sha256 = "sha256-FEa9QjQoGNUOAtMNMZcqpTKMKVtXoBuOomTy0mpos/0="; fetchSubmodules = true; }; - patches = [ - # make ldc 1.27.1 compatible - (fetchpatch { - url = "https://github.com/biod/sambamba/pull/480/commits/b5c80feb62683d24ec0529f685a1d7a36962a1d4.patch"; - sha256 = "0yr9baxqbhyb4scwcwczk77z8gazhkl60jllhz9dnrb7p5qsvs7r"; - }) - ]; - nativeBuildInputs = [ which python3 ldc ]; - buildInputs = [ zlib ]; + buildInputs = [ zlib lz4 ]; # Upstream's install target is broken; copy manually installPhase = '' diff --git a/pkgs/applications/science/biology/spades/default.nix b/pkgs/applications/science/biology/spades/default.nix index b41d266dbab58..5302b43bb0263 100644 --- a/pkgs/applications/science/biology/spades/default.nix +++ b/pkgs/applications/science/biology/spades/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "SPAdes"; - version = "3.15.3"; + version = "3.15.4"; src = fetchurl { url = "http://cab.spbu.ru/files/release${version}/${pname}-${version}.tar.gz"; - sha256 = "sha256-suWp/XplruWriGIi1q9Pe3vH91XaegOUFXH6vWueFJk="; + sha256 = "sha256-OyQcUopCqL398j5b+PAISDR5BZDQhJHezqnw8AnYWJ8="; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/biology/stacks/default.nix b/pkgs/applications/science/biology/stacks/default.nix index 89ac4c49629e6..5fcb367ce5cb1 100644 --- a/pkgs/applications/science/biology/stacks/default.nix +++ b/pkgs/applications/science/biology/stacks/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "stacks"; - version = "2.59"; + version = "2.60"; src = fetchurl { url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz"; - sha256 = "sha256-pVFwb4EPba9wL9kDGN2gi7aeH+sPhDG/XLyHxqG4zd4="; + sha256 = "sha256-ppKG7Z1TyLwUyqRnGYk3QWPJqKeNcW04GMW7myPFSNM="; }; buildInputs = [ zlib ]; diff --git a/pkgs/applications/science/biology/star/default.nix b/pkgs/applications/science/biology/star/default.nix index 4328bbd975a89..3555929a33eaf 100644 --- a/pkgs/applications/science/biology/star/default.nix +++ b/pkgs/applications/science/biology/star/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "star"; - version = "2.7.9a"; + version = "2.7.10a"; src = fetchFromGitHub { repo = "STAR"; owner = "alexdobin"; rev = version; - sha256 = "sha256-p1yaIbSGu8K5AkqJj0BAzuoWsXr25eCNoQmLXYQeg4E="; + sha256 = "sha256-qwddCGMOKWgx76qGwRQXwvv9fCSeVsZbWHmlBwEqGKE="; }; sourceRoot = "source/source"; diff --git a/pkgs/applications/science/biology/tebreak/default.nix b/pkgs/applications/science/biology/tebreak/default.nix index cb606a6b34635..e56d91dc2cd12 100644 --- a/pkgs/applications/science/biology/tebreak/default.nix +++ b/pkgs/applications/science/biology/tebreak/default.nix @@ -1,7 +1,7 @@ -{ lib, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa -, samtools, findutils, python }: +{ lib, fetchFromGitHub, last, exonerate, minia, python3, bwa +, samtools, findutils }: -python3Packages.buildPythonApplication rec { +python3.pkgs.buildPythonApplication rec { pname = "tebreak"; version = "1.1"; @@ -12,8 +12,8 @@ python3Packages.buildPythonApplication rec { sha256 = "13mgh775d8hkl340923lfwwm4r5ps70girn8d6wgfxzwzxylz8iz"; }; - nativeBuildInputs = [ findutils python3Packages.cython ]; - propagatedBuildInputs = with python3Packages; [ + nativeBuildInputs = [ findutils python3.pkgs.cython ]; + propagatedBuildInputs = with python3.pkgs; [ pysam scipy bx-python @@ -35,7 +35,7 @@ python3Packages.buildPythonApplication rec { checkPhase = '' $out/bin/tebreak -b test/data/example.ins.bam -r test/data/Homo_sapiens_chr4_50000000-60000000_assembly19.fasta -p 4 --pickle test/example.pickle --detail_out test/example.tebreak.detail.out -i lib/teref.human.fa pushd test - ${python.interpreter} checktest.py + ${python3.interpreter} checktest.py ''; meta = with lib; { diff --git a/pkgs/applications/science/biology/xenomapper/default.nix b/pkgs/applications/science/biology/xenomapper/default.nix index f5e538c70961e..194db966915e1 100644 --- a/pkgs/applications/science/biology/xenomapper/default.nix +++ b/pkgs/applications/science/biology/xenomapper/default.nix @@ -1,6 +1,6 @@ -{buildPythonPackage, lib, fetchFromGitHub, statistics}: +{ python3, lib, fetchFromGitHub }: -buildPythonPackage rec { +python3.pkgs.buildPythonApplication rec { pname = "xenomapper"; version = "1.0.2"; @@ -11,7 +11,7 @@ buildPythonPackage rec { sha256 = "0mnmfzlq5mhih6z8dq5bkx95vb8whjycz9mdlqwbmlqjb3gb3zhr"; }; - propagatedBuildInputs = [ statistics ]; + propagatedBuildInputs = with python3.pkgs; [ statistics ]; meta = with lib; { homepage = "https://github.com/genomematt/xenomapper"; |