diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology')
33 files changed, 286 insertions, 118 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix b/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix index 7502a4ffd2ab..a9661ee2db78 100644 --- a/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix @@ -2,7 +2,7 @@ stdenv.mkDerivation rec { pname = "EZminc"; - name = "${pname}-unstable-2019-03-12"; + version = "unstable-2019-03-12"; src = fetchFromGitHub { owner = "BIC-MNI"; @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake pkgconfig ]; buildInputs = [ itk4 libminc bicpl fftwFloat gsl ]; - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEZMINC_BUILD_TOOLS=TRUE" "-DEZMINC_BUILD_MRFSEG=TRUE" "-DEZMINC_BUILD_DD=TRUE" ]; diff --git a/nixpkgs/pkgs/applications/science/biology/N3/default.nix b/nixpkgs/pkgs/applications/science/biology/N3/default.nix index d2dbcf185330..13ffc305d392 100644 --- a/nixpkgs/pkgs/applications/science/biology/N3/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/N3/default.nix @@ -4,20 +4,20 @@ stdenv.mkDerivation rec { pname = "N3"; - name = "${pname}-2017-09-18"; + version = "unstable-2018-08-09"; src = fetchFromGitHub { owner = "BIC-MNI"; repo = pname; - rev = "2fdd939f0f2b24a4039bc6a8ade4a190a1d8e75d"; - sha256 = "13z21c4r09hna3q1csvcn4i7ws5ixbdaja6ch421xv6nydjh2w5g"; + rev = "010fc2ac58ce1d67b8e6a863fac0809d3203cb9b"; + sha256 = "06hci7gzhy8p34ggvx7gah2k9yxpwhgmq1cgw8pcd1r82g4rg6kd"; }; nativeBuildInputs = [ cmake makeWrapper ]; buildInputs = [ libminc EBTKS ]; propagatedBuildInputs = with perlPackages; [ perl MNI-Perllib GetoptTabular ]; - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ]; + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${EBTKS}/lib/" ]; postFixup = '' for p in $out/bin/*; do @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { - homepage = "https://github.com/BIC-MNI/${pname}"; + homepage = "https://github.com/BIC-MNI/N3"; description = "MRI non-uniformity correction for MINC files"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; diff --git a/nixpkgs/pkgs/applications/science/biology/ants/default.nix b/nixpkgs/pkgs/applications/science/biology/ants/default.nix index cb88e92fe1cb..ece218eea37d 100644 --- a/nixpkgs/pkgs/applications/science/biology/ants/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/ants/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, itk4, vtk_7 }: +{ stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, itk4, vtk_7, Cocoa }: stdenv.mkDerivation rec { pname = "ANTs"; @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { ]; nativeBuildInputs = [ cmake makeWrapper ]; - buildInputs = [ itk4 vtk_7 ]; + buildInputs = [ itk4 vtk_7 ] ++ stdenv.lib.optional stdenv.isDarwin [ Cocoa ]; cmakeFlags = [ "-DANTS_SUPERBUILD=FALSE" "-DUSE_VTK=TRUE" ]; diff --git a/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix b/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix index b847fd8b5fe4..d1b033dc4e23 100644 --- a/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "bcftools"; - version = "1.10.2"; + version = "1.11"; src = fetchurl { url = "https://github.com/samtools/bcftools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "0b2f6lqhxdlrvfjqxv7a4nzqj68c1j4avn16iqxwwm80kn302wzm"; + sha256 = "0r508mp15pqzf8r1269kb4v5naw9zsvbwd3cz8s1yj7carsf9viw"; }; buildInputs = [ htslib zlib bzip2 lzma curl perl python ]; diff --git a/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix index 332e06ea0cf5..f92e912f6800 100644 --- a/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} install"; meta = with stdenv.lib; { - description = "A powerful toolset for genome arithmetic."; + description = "A powerful toolset for genome arithmetic"; license = licenses.gpl2; homepage = "https://bedtools.readthedocs.io/en/latest/"; maintainers = with maintainers; [ jbedo ]; diff --git a/nixpkgs/pkgs/applications/science/biology/bowtie/default.nix b/nixpkgs/pkgs/applications/science/biology/bowtie/default.nix new file mode 100644 index 000000000000..964eeddb461d --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/bowtie/default.nix @@ -0,0 +1,25 @@ +{ stdenv, fetchFromGitHub, zlib }: + +stdenv.mkDerivation rec { + pname = "bowtie"; + version = "1.3.0"; + + src = fetchFromGitHub { + owner = "BenLangmead"; + repo = pname; + rev = "v${version}"; + sha256 = "0da2kzyfsn6xv8mlqsv2vv7k8g0c9d2vgqzq8yqk888yljdzcrjp"; + }; + + buildInputs = [ zlib ]; + + installFlags = [ "prefix=$(out)" ]; + + meta = with stdenv.lib; { + description = "An ultrafast memory-efficient short read aligner"; + license = licenses.artistic2; + homepage = "http://bowtie-bio.sf.net/bowtie"; + maintainers = with maintainers; [ prusnak ]; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix index dc818e2fb868..603e5892ff11 100644 --- a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix @@ -1,19 +1,19 @@ -{ stdenv, fetchFromGitHub, zlib, tbb, python, perl }: +{ stdenv, fetchFromGitHub, cmake, tbb, zlib }: stdenv.mkDerivation rec { pname = "bowtie2"; - version = "2.3.5.1"; + version = "2.4.2"; src = fetchFromGitHub { owner = "BenLangmead"; repo = pname; rev = "v${version}"; - sha256 = "1l1f0yhjqqvy4lpxfml1xwv7ayimwbpzazvp0281gb4jb5f5mr1a"; + sha256 = "11apzq7l1lk3yxw97g9dfr0gwnvfh58x6apifcblgd66gbip3y1y"; }; - buildInputs = [ zlib tbb python perl ]; + nativeBuildInputs = [ cmake ]; - installFlags = [ "prefix=$(out)" ]; + buildInputs = [ tbb zlib ]; meta = with stdenv.lib; { description = "An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences"; @@ -21,6 +21,6 @@ stdenv.mkDerivation rec { homepage = "http://bowtie-bio.sf.net/bowtie2"; maintainers = with maintainers; [ rybern ]; platforms = platforms.all; - broken = stdenv.isAarch64; + broken = stdenv.isAarch64; # only x86 is supported }; } diff --git a/nixpkgs/pkgs/applications/science/biology/bwa/default.nix b/nixpkgs/pkgs/applications/science/biology/bwa/default.nix index 7212b42198c4..10859d9e8c13 100644 --- a/nixpkgs/pkgs/applications/science/biology/bwa/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bwa/default.nix @@ -11,6 +11,12 @@ stdenv.mkDerivation rec { buildInputs = [ zlib ]; + # Avoid hardcoding gcc to allow environments with a different + # C compiler to build + preConfigure = '' + sed -i '/^CC/d' Makefile + ''; + # it's unclear which headers are intended to be part of the public interface # so we may find ourselves having to add more here over time installPhase = '' @@ -27,6 +33,6 @@ stdenv.mkDerivation rec { license = licenses.gpl3; homepage = "http://bio-bwa.sourceforge.net/"; maintainers = with maintainers; [ luispedro ]; - platforms = [ "x86_64-linux" ]; + platforms = platforms.x86_64; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix b/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix index 971e2f23055b..8fb8e17eef86 100644 --- a/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix @@ -3,7 +3,7 @@ stdenv.mkDerivation rec { pname = "conglomerate"; - name = "${pname}-2017-09-10"; + version = "unstable-2017-09-10"; src = fetchFromGitHub { owner = "BIC-MNI"; @@ -16,7 +16,10 @@ stdenv.mkDerivation rec { buildInputs = [ libminc zlib bicpl ]; propagatedBuildInputs = [ coreutils minc_tools ] ++ (with perlPackages; [ perl GetoptTabular MNI-Perllib ]); - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBICPL_DIR=${bicpl}/lib/" ]; + cmakeFlags = [ + "-DLIBMINC_DIR=${libminc}/lib/cmake" + "-DBICPL_DIR=${bicpl}/lib" + ]; postFixup = '' for p in $out/bin/*; do diff --git a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix index 59b173ac98cd..cfd1206f2314 100644 --- a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { buildInputs = [ libyamlcpp ]; meta = with stdenv.lib; { - description = "dcm2niix DICOM to NIfTI converter"; + description = "DICOM to NIfTI converter"; longDescription = '' dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format. diff --git a/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix b/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix index 8787c96e5b03..2621c5bbf037 100644 --- a/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix @@ -1,14 +1,14 @@ -{ lib -, python -}: +{ lib, python, fetchFromGitHub }: with python.pkgs; buildPythonApplication rec { pname = "deepTools"; - version = "3.4.1"; + version = "3.5.0"; - src = fetchPypi { - inherit pname version; - sha256 = "05zw9gk17hz08hns5lnhn7l13idg9jdz4gdba6m6gbr84yz149gs"; + src = fetchFromGitHub { + owner = "deeptools"; + repo = "deepTools"; + rev = version; + sha256 = "1bz8ln32mfc9k8l9wgp034vw80dxh6f92dfqxhcrpggk4akwj6ml"; }; propagatedBuildInputs = [ @@ -23,7 +23,7 @@ buildPythonApplication rec { deeptoolsintervals ]; - checkInputs = [ pytest ]; + checkInputs = [ nose ]; meta = with lib; { homepage = "https://deeptools.readthedocs.io/en/develop"; diff --git a/nixpkgs/pkgs/applications/science/biology/delly/default.nix b/nixpkgs/pkgs/applications/science/biology/delly/default.nix index a6c45f8aa44e..8f4dd7745269 100644 --- a/nixpkgs/pkgs/applications/science/biology/delly/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/delly/default.nix @@ -1,25 +1,16 @@ { stdenv, fetchpatch, fetchFromGitHub, htslib, zlib, bzip2, lzma, ncurses, boost }: -let - htslibPatch = fetchpatch { - url = "https://github.com/dellytools/delly/commit/0e5c710b0c5ea790bb39699d4cbd49cf4fb86f14.diff"; - sha256 = "09bz1qqvzhdzm99hf9zgrv80kq9jlr1m2mdvx96p2hk5lpnbdl7y"; - excludes = [ "src/htslib" ]; - }; - -in stdenv.mkDerivation rec { +stdenv.mkDerivation rec { pname = "delly"; - version = "0.8.2"; + version = "0.8.6"; src = fetchFromGitHub { owner = "dellytools"; repo = pname; rev = "v${version}"; - sha256 = "14bkmixz7737xj192ww96s3a20zc7xs7r04db8avw3ggi3i1s1cs"; + sha256 = "sha256-j9klZ8qq1GQS7+zZ+vHwAwLHBYMBrWfbwqeD8QJeCuk="; }; - patches = [ htslibPatch ]; - buildInputs = [ zlib htslib bzip2 lzma ncurses boost ]; EBROOTHTSLIB = htslib; @@ -34,7 +25,7 @@ in stdenv.mkDerivation rec { meta = with stdenv.lib; { description = "Structural variant caller for mapped DNA sequenced data"; - license = licenses.gpl3; + license = licenses.bsd3; maintainers = with maintainers; [ scalavision ]; platforms = platforms.linux; longDescription = '' diff --git a/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix b/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix index 6ee7cd609c42..3b1420a18819 100644 --- a/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix @@ -1,12 +1,12 @@ { stdenv, fetchurl }: stdenv.mkDerivation rec { - version = "3.3.1"; + version = "3.3.2"; pname = "hmmer"; src = fetchurl { url = "http://eddylab.org/software/hmmer/${pname}-${version}.tar.gz"; - sha256 = "1mcvr74w6ffd5z0p8v3jss473mbgard9lz5whjnk95c661lnmrlc"; + sha256 = "0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj"; }; meta = with stdenv.lib; { diff --git a/nixpkgs/pkgs/applications/science/biology/igv/default.nix b/nixpkgs/pkgs/applications/science/biology/igv/default.nix index bc4f1677fc98..3f9cb1a288b3 100644 --- a/nixpkgs/pkgs/applications/science/biology/igv/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/igv/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "igv"; - version = "2.8.9"; + version = "2.8.13"; src = fetchzip { url = "https://data.broadinstitute.org/igv/projects/downloads/2.8/IGV_${version}.zip"; - sha256 = "1874w1xprv91caz1ymfxilq6inhj36xzx8j9m0mcyp0qfvfvyjp7"; + sha256 = "0sab478jq96iw3fv0560hrrj8qbh40r8m4ncypdb7991j9haxl09"; }; installPhase = '' diff --git a/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix b/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix index 9e63b92b24ed..e6293bb90ef3 100644 --- a/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { buildInputs = [ libminc EBTKS ]; propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ]; - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ]; + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${EBTKS}/lib/" ]; postFixup = '' for p in $out/bin/*; do diff --git a/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix b/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix index 5a1bb187886b..014ae14cc794 100644 --- a/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = false; meta = with stdenv.lib; { - description = "Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data"; + description = "Program for quantifying abundances of transcripts from RNA-Seq data"; homepage = "https://pachterlab.github.io/kallisto"; license = licenses.bsd2; platforms = platforms.linux; diff --git a/nixpkgs/pkgs/applications/science/biology/kent/default.nix b/nixpkgs/pkgs/applications/science/biology/kent/default.nix new file mode 100644 index 000000000000..2ca5ad191d92 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/kent/default.nix @@ -0,0 +1,75 @@ +{ stdenv +, libpng +, libuuid +, zlib +, bzip2 +, lzma +, openssl +, curl +, libmysqlclient +, bash +, fetchFromGitHub +, which +}: +stdenv.mkDerivation rec { + pname = "kent"; + version = "404"; + + src = fetchFromGitHub { + owner = "ucscGenomeBrowser"; + repo = pname; + rev = "v${version}_base"; + sha256 = "0l5lmqqc6sqkf4hyk3z4825ly0vdlj5xdfad6zd0708cb1v81nbx"; + }; + + buildInputs = [ libpng libuuid zlib bzip2 lzma openssl curl libmysqlclient ]; + + patchPhase = '' + substituteInPlace ./src/checkUmask.sh \ + --replace "/bin/bash" "${bash}/bin/bash" + + substituteInPlace ./src/hg/sqlEnvTest.sh \ + --replace "which mysql_config" "${which}/bin/which ${libmysqlclient}/bin/mysql_config" + ''; + + buildPhase = '' + export MACHTYPE=$(uname -m) + export CFLAGS="-fPIC" + export MYSQLINC=$(mysql_config --include | sed -e 's/^-I//g') + export MYSQLLIBS=$(mysql_config --libs) + export DESTBINDIR=$NIX_BUILD_TOP/bin + export HOME=$NIX_BUILD_TOP + + cd ./src + chmod +x ./checkUmask.sh + ./checkUmask.sh + + mkdir -p $NIX_BUILD_TOP/lib + mkdir -p $NIX_BUILD_TOP/bin/x86_64 + + make libs + cd jkOwnLib + make + + cp ../lib/x86_64/jkOwnLib.a $NIX_BUILD_TOP/lib + cp ../lib/x86_64/jkweb.a $NIX_BUILD_TOP/lib + + cd ../utils + make + ''; + + installPhase = '' + mkdir -p $out/bin + mkdir -p $out/lib + cp $NIX_BUILD_TOP/lib/jkOwnLib.a $out/lib + cp $NIX_BUILD_TOP/lib/jkweb.a $out/lib + cp $NIX_BUILD_TOP/bin/x86_64/* $out/bin + ''; + + meta = with stdenv.lib; { + description = "UCSC Genome Bioinformatics Group's suite of biological analysis tools, i.e. the kent utilities"; + license = licenses.unfree; + maintainers = with maintainers; [ scalavision ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/last/default.nix b/nixpkgs/pkgs/applications/science/biology/last/default.nix index 13f6a23913fc..0976e5a10802 100644 --- a/nixpkgs/pkgs/applications/science/biology/last/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/last/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1066"; + version = "1145"; src = fetchurl { url = "http://last.cbrc.jp/last-${version}.zip"; - sha256 = "098j3f3a80rmhd01ds7rnb9y1xykmll2yh5ivpnvskssd8z2vc4r"; + sha256 = "0g54nmxxrirgid1i1k5i6rf7vnjpk9548sy06yqb4fj7vdzqgq99"; }; nativeBuildInputs = [ unzip ]; diff --git a/nixpkgs/pkgs/applications/science/biology/lumpy/default.nix b/nixpkgs/pkgs/applications/science/biology/lumpy/default.nix new file mode 100644 index 000000000000..f6267a2e017f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/lumpy/default.nix @@ -0,0 +1,50 @@ +{ 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 stdenv.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/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix index b2029842bbba..c594897f4b6f 100644 --- a/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix @@ -3,28 +3,20 @@ stdenv.mkDerivation rec { pname = "minc-tools"; - version = "unstable-2019-12-04"; + version = "unstable-2020-07-25"; src = fetchFromGitHub { owner = "BIC-MNI"; repo = pname; - rev = "d4dddfdb4e4fa0cea389b8fdce51cfc076565d94"; - sha256 = "1wwdss59qq4hz1jp35qylfswzzv0d37if23al0srnxkkgc5f8zng"; + rev = "fb0a68a07d281e4e099c5d54df29925240de14c1"; + sha256 = "0zcv2sdj3k6k0xjqdq8j5bxq8smm48dzai90vwsmz8znmbbm6kvw"; }; - patches = [ ./fix-netcdf-header.patch ]; - - # add missing CMake module to build NIFTI support - # (the maintainers normally build libminc and minc-tools in a meta-project) - postPatch = '' - cp ${libminc.src}/cmake-modules/FindNIFTI.cmake cmake-modules - ''; - nativeBuildInputs = [ cmake flex bison makeWrapper ]; buildInputs = [ libminc libjpeg nifticlib zlib ]; propagatedBuildInputs = [ perl TextFormat ]; - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DZNZ_INCLUDE_DIR=${nifticlib}/include/nifti" "-DNIFTI_INCLUDE_DIR=${nifticlib}/include/nifti" ]; diff --git a/nixpkgs/pkgs/applications/science/biology/minc-tools/fix-netcdf-header.patch b/nixpkgs/pkgs/applications/science/biology/minc-tools/fix-netcdf-header.patch deleted file mode 100644 index 89c7564f8b62..000000000000 --- a/nixpkgs/pkgs/applications/science/biology/minc-tools/fix-netcdf-header.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/progs/mincdump/mincdump.h b/progs/mincdump/mincdump.h -index 14c95cd..117ab26 100644 ---- a/progs/mincdump/mincdump.h -+++ b/progs/mincdump/mincdump.h -@@ -3,6 +3,7 @@ - * See netcdf/COPYRIGHT file for copying and redistribution conditions. - * $Header: /private-cvsroot/minc/progs/mincdump/mincdump.h,v 1.1 2004-04-27 15:35:15 bert Exp $ - *********************************************************************/ -+#include <netcdf_meta.h> - - - /* error checking macro */ diff --git a/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix b/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix index 254d874f9d91..40ec9e0de6d2 100644 --- a/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix @@ -2,7 +2,7 @@ stdenv.mkDerivation rec { pname = "mni_autoreg"; - name = "${pname}-2017-09-22"; + version = "unstable-2017-09-22"; src = fetchFromGitHub { owner = "BIC-MNI"; @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { buildInputs = [ libminc ]; propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ]; - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ]; + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" ]; # testing broken: './minc_wrapper: Permission denied' from Testing/ellipse0.mnc postFixup = '' diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix index 1ce6357d2e81..d2b05943f7ce 100644 --- a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix @@ -17,13 +17,13 @@ let in stdenv.mkDerivation rec { pname = "mosdepth"; - version = "0.2.9"; + version = "0.3.1"; src = fetchFromGitHub { owner = "brentp"; repo = "mosdepth"; rev = "v${version}"; - sha256 = "01gm9gj2x2zs4yx6wk761fi1papi7qr3gp4ln1kkn8n2f9y9h849"; + sha256 = "1kcrvamrafz1m0s7mlbhaay8jyg97l1w37p6syl36r2m1plmwxjd"; }; nativeBuildInputs = [ nim ]; @@ -37,7 +37,7 @@ in stdenv.mkDerivation rec { installPhase = "install -Dt $out/bin mosdepth"; meta = with stdenv.lib; { - description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing."; + description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing"; license = licenses.mit; homepage = "https://github.com/brentp/mosdepth"; maintainers = with maintainers; [ jbedo ]; diff --git a/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix b/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix index 528277e05e38..e0b122778d1b 100644 --- a/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/mrtrix/default.nix @@ -5,13 +5,13 @@ stdenv.mkDerivation rec { pname = "mrtrix"; - version = "3.0.0"; + version = "3.0.2"; src = fetchFromGitHub { owner = "MRtrix3"; repo = "mrtrix3"; rev = version; - sha256 = "1vvmmbw3m0bdfwp4szr62ygzsvkj0ss91cx5zlkspsr1rff05f9b"; + sha256 = "0p4d1230j6664rnb9l65cpyfj9ncbcm39yv1r9y77br9rkkv1za3"; fetchSubmodules = true; }; diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix index d496e78748d9..af29dd77ac28 100644 --- a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.23.4"; + version = "2.23.9"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "0xg4nbx02a2kckr6p8pqjpv5rmp95bkmglgm1bma6f77s7hkab7q"; + sha256 = "1ygdl590sbcsxpk0qwr0bx163nx51h0545n1xxkbc3pk2r6n51lk"; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/biology/plink/default.nix b/nixpkgs/pkgs/applications/science/biology/plink/default.nix deleted file mode 100644 index 009e12aa02f0..000000000000 --- a/nixpkgs/pkgs/applications/science/biology/plink/default.nix +++ /dev/null @@ -1,25 +0,0 @@ -{ stdenv, fetchurl, zlib, unzip }: - -stdenv.mkDerivation { - name = "plink-1.07"; - - src = fetchurl { - url = "http://pngu.mgh.harvard.edu/~purcell/plink/dist/plink-1.07-src.zip"; - sha256 = "4af56348443d0c6a1db64950a071b1fcb49cc74154875a7b43cccb4b6a7f482b"; - }; - - buildInputs = [ zlib unzip ] ; - - installPhase = '' - mkdir -p $out/bin - cp plink $out/bin - ''; - - meta = { - description = "Whole genome association toolkit"; - homepage = "http://pngu.mgh.harvard.edu/~purcell/plink/"; - license = stdenv.lib.licenses.gpl2; - platforms = stdenv.lib.platforms.all; - broken = true; - }; -} diff --git a/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix b/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix new file mode 100644 index 000000000000..7e33a6612189 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/sambamba/default.nix @@ -0,0 +1,31 @@ +{ stdenv, fetchFromGitHub, python3, which, dmd, ldc, zlib }: + +stdenv.mkDerivation rec { + pname = "sambamba"; + version = "0.7.1"; + + src = fetchFromGitHub { + owner = "biod"; + repo = "sambamba"; + rev = "v${version}"; + sha256 = "0k5wy06zrbsc40x6answgz7rz2phadyqwlhi9nqxbfqanbg9kq20"; + fetchSubmodules = true; + }; + + nativeBuildInputs = [ which python3 dmd ldc ]; + buildInputs = [ zlib ]; + + # Upstream's install target is broken; copy manually + installPhase = '' + mkdir -p $out/bin + cp bin/sambamba-${version} $out/bin/sambamba + ''; + + meta = with stdenv.lib; { + description = "SAM/BAM processing tool"; + homepage = "https://lomereiter.github.io/sambamba/"; + maintainers = with maintainers; [ jbedo ]; + license = with licenses; gpl2; + platforms = platforms.x86_64; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix b/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix new file mode 100644 index 000000000000..6846e3c84fae --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix @@ -0,0 +1,26 @@ +{ stdenv, fetchFromGitHub }: + +stdenv.mkDerivation rec { + pname = "samblaster"; + version = "0.1.26"; + + src = fetchFromGitHub { + owner = "GregoryFaust"; + repo = "samblaster"; + rev = "v.${version}"; + sha256 = "0g24fq5hplnfgqkh3xqpg3lgx3wmxwnh9c7m6yw7pbi40lmgl1jv"; + }; + + installPhase = '' + mkdir -p $out/bin + cp samblaster $out/bin + ''; + + meta = with stdenv.lib; { + description = "Tool for marking duplicates and extracting discordant/split reads from SAM/BAM files"; + maintainers = with maintainers; [ jbedo ]; + license = licenses.mit; + homepage = "https://github.com/GregoryFaust/samblaster"; + platforms = platforms.x86_64; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/samtools/default.nix b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix index e750eea89ac9..27ed79a1f6ca 100644 --- a/nixpkgs/pkgs/applications/science/biology/samtools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "samtools"; - version = "1.10"; + version = "1.11"; src = fetchurl { url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv"; + sha256 = "1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2"; }; nativeBuildInputs = [ perl ]; @@ -29,6 +29,6 @@ stdenv.mkDerivation rec { license = licenses.mit; homepage = "http://www.htslib.org/"; platforms = platforms.unix; - maintainers = [ maintainers.mimame ]; + maintainers = with maintainers; [ mimame unode ]; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix b/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix index c68fcfada332..941f107a580f 100644 --- a/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { ''; meta = with stdenv.lib; { - description = "Genetic variant annotation and effect prediction toolbox."; + description = "Genetic variant annotation and effect prediction toolbox"; license = licenses.lgpl3; homepage = "http://snpeff.sourceforge.net/"; maintainers = with maintainers; [ jbedo ]; diff --git a/nixpkgs/pkgs/applications/science/biology/spades/default.nix b/nixpkgs/pkgs/applications/science/biology/spades/default.nix index d555f2873a67..776719579d97 100644 --- a/nixpkgs/pkgs/applications/science/biology/spades/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/spades/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, zlib, bzip2, cmake }: +{ stdenv, fetchurl, zlib, bzip2, cmake, python3 }: stdenv.mkDerivation rec { pname = "SPAdes"; @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; - buildInputs = [ zlib bzip2 ]; + buildInputs = [ zlib bzip2 python3 ]; doCheck = true; diff --git a/nixpkgs/pkgs/applications/science/biology/star/default.nix b/nixpkgs/pkgs/applications/science/biology/star/default.nix index c331acbfe705..f2e1a2a8fee5 100644 --- a/nixpkgs/pkgs/applications/science/biology/star/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/star/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "star"; - version = "2.7.5c"; + version = "2.7.6a"; src = fetchFromGitHub { repo = "STAR"; owner = "alexdobin"; rev = version; - sha256 = "1plx9akrzwjk7f2j94l9ss0apg0asqmrf2bp0728d4bvlhnzmjyy"; + sha256 = "1zw9f4jbhz0y51namnmid42pa7pviviy94q9db8w0774nksdf8is"; }; sourceRoot = "source/source"; diff --git a/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix b/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix index 07669d097a44..82c624ba7cd9 100644 --- a/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix @@ -1,5 +1,5 @@ { stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa -, samtools, findutils }: +, samtools, findutils, python }: python3Packages.buildPythonApplication rec { pname = "tebreak"; @@ -32,6 +32,12 @@ python3Packages.buildPythonApplication rec { done ''; + 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 + ''; + meta = with stdenv.lib; { description = "Find and characterise transposable element insertions"; homepage = "https://github.com/adamewing/tebreak"; |