diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology')
12 files changed, 65 insertions, 24 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/N3/default.nix b/nixpkgs/pkgs/applications/science/biology/N3/default.nix index 3502ac3e51b7..d2dbcf185330 100644 --- a/nixpkgs/pkgs/applications/science/biology/N3/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/N3/default.nix @@ -1,5 +1,5 @@ { stdenv, fetchFromGitHub, cmake, makeWrapper, - perl, MNI-Perllib, GetoptTabular, + perlPackages, libminc, EBTKS }: stdenv.mkDerivation rec { @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake makeWrapper ]; buildInputs = [ libminc EBTKS ]; - propagatedBuildInputs = [ perl MNI-Perllib GetoptTabular ]; + propagatedBuildInputs = with perlPackages; [ perl MNI-Perllib GetoptTabular ]; cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ]; diff --git a/nixpkgs/pkgs/applications/science/biology/bftools/default.nix b/nixpkgs/pkgs/applications/science/biology/bftools/default.nix new file mode 100644 index 000000000000..24a6e052df9e --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/bftools/default.nix @@ -0,0 +1,41 @@ +{ stdenv, lib, makeWrapper, fetchzip, jre }: + +stdenv.mkDerivation rec { + name = "bftools-${version}"; + version = "5.9.2"; + + src = fetchzip { + url = "http://downloads.openmicroscopy.org/bio-formats/${version}/artifacts/bftools.zip"; + sha256 = "08lmbg3kfxh17q6548il0i2h3f9a6ch8r0r067p14dajhzfpjyqj"; + }; + + installPhase = '' + find . -maxdepth 1 -perm -111 -type f -not -name "*.sh" \ + -exec install -vD {} "$out"/bin/{} \; + + mkdir $out/libexec + mkdir -p $out/share/java + + cp ./*.sh $out/libexec + cp ./*.jar $out/share/java + + for file in $out/bin/*; do + substituteInPlace $file --replace "\$BF_DIR" $out/libexec + done + substituteInPlace $out/libexec/bf.sh --replace "\$BF_JAR_DIR" $out/share/java + ''; + + postFixup = '' + wrapProgram $out/libexec/bf.sh --prefix PATH : "${lib.makeBinPath [ jre ]}" + ''; + + nativeBuildInputs = [ makeWrapper ]; + + meta = with stdenv.lib; { + description = "A bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already included"; + license = licenses.gpl2; + platforms = platforms.all; + homepage = https://www.openmicroscopy.org/bio-formats/; + maintainers = [ maintainers.tbenst ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix b/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix index c04bc84c156d..23182fcadc6b 100644 --- a/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix @@ -1,5 +1,5 @@ -{ stdenv, fetchFromGitHub, cmake, coreutils, perl, bicpl, libminc, zlib, minc_tools, - makeWrapper, GetoptTabular, MNI-Perllib }: +{ stdenv, fetchFromGitHub, cmake, coreutils, perlPackages, bicpl, libminc, zlib, minc_tools, + makeWrapper }: stdenv.mkDerivation rec { pname = "conglomerate"; @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake makeWrapper ]; buildInputs = [ libminc zlib bicpl ]; - propagatedBuildInputs = [ coreutils minc_tools perl GetoptTabular MNI-Perllib ]; + propagatedBuildInputs = [ coreutils minc_tools ] ++ (with perlPackages; [ perl GetoptTabular MNI-Perllib ]); cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBICPL_DIR=${bicpl}/lib/" ]; diff --git a/nixpkgs/pkgs/applications/science/biology/igv/default.nix b/nixpkgs/pkgs/applications/science/biology/igv/default.nix index 1804f854c48c..19ba508d758e 100644 --- a/nixpkgs/pkgs/applications/science/biology/igv/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/igv/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "igv-${version}"; - version = "2.4.16"; + version = "2.4.17"; src = fetchurl { url = "https://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_${version}.zip"; - sha256 = "0bsl20zw7sgw16xadh1hmlg6d6ijyb1dhpnyvf4kxk3nk0abrmn1"; + sha256 = "02zl0r1yhyllh000cad6pjk0ic0xm6l05jzkglsf8wdz17nh15nr"; }; buildInputs = [ unzip jre ]; diff --git a/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix b/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix index 7ba054a592ea..9e63b92b24ed 100644 --- a/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix @@ -1,5 +1,5 @@ { stdenv, fetchFromGitHub, cmake, makeWrapper, - perl, GetoptTabular, MNI-Perllib, + perlPackages, libminc, EBTKS }: stdenv.mkDerivation rec { @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake makeWrapper ]; buildInputs = [ libminc EBTKS ]; - propagatedBuildInputs = [ perl GetoptTabular MNI-Perllib ]; + propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ]; cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ]; diff --git a/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix index c680eda95d2f..033f78609e9a 100644 --- a/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, makeWrapper, flex, bison, perl, TextFormat, libminc, libjpeg, zlib }: +{ stdenv, fetchFromGitHub, cmake, makeWrapper, flex, bison, perlPackages, libminc, libjpeg, zlib }: stdenv.mkDerivation rec { pname = "minc-tools"; @@ -13,7 +13,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake flex bison makeWrapper ]; buildInputs = [ libminc libjpeg zlib ]; - propagatedBuildInputs = [ perl TextFormat ]; + propagatedBuildInputs = with perlPackages; [ perl TextFormat ]; cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ]; diff --git a/nixpkgs/pkgs/applications/science/biology/minc-widgets/default.nix b/nixpkgs/pkgs/applications/science/biology/minc-widgets/default.nix index 9084dfb2e1c3..497c39a52a4c 100644 --- a/nixpkgs/pkgs/applications/science/biology/minc-widgets/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/minc-widgets/default.nix @@ -1,5 +1,5 @@ { stdenv, fetchFromGitHub, cmake, makeWrapper, - perl, GetoptTabular, MNI-Perllib, + perlPackages, libminc, octave, coreutils, minc_tools }: stdenv.mkDerivation rec { @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake makeWrapper ]; buildInputs = [ libminc ]; - propagatedBuildInputs = [ perl GetoptTabular MNI-Perllib octave coreutils minc_tools ]; + propagatedBuildInputs = (with perlPackages; [ perl GetoptTabular MNI-Perllib ]) ++ [ octave coreutils minc_tools ]; postFixup = '' for p in $out/bin/*; do diff --git a/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix b/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix index ae278f76792b..3f28b5e31ccd 100644 --- a/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix @@ -3,13 +3,13 @@ stdenv.mkDerivation rec { name = "${pname}-${version}"; pname = "minimap2"; - version = "2.10"; + version = "2.15"; src = fetchFromGitHub { repo = pname; owner = "lh3"; rev = "v${version}"; - sha256 = "0b35w14j9h2q9qbh3sxc518mcx0ifsvwqr1nv70rv6mgy1cqqkw0"; + sha256 = "0dy3m2wjmi3whjnmkj3maa1aadz525h7736wm8vvdcwq71ijqb7v"; }; buildInputs = [ zlib ]; diff --git a/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix b/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix index 076ecd03a1b1..5901b696d642 100644 --- a/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, makeWrapper, perl, GetoptTabular, MNI-Perllib, libminc }: +{ stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, libminc }: stdenv.mkDerivation rec { pname = "mni_autoreg"; @@ -13,7 +13,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake makeWrapper ]; buildInputs = [ libminc ]; - propagatedBuildInputs = [ perl GetoptTabular MNI-Perllib ]; + propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ]; cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBUILD_TESTING=FALSE" ]; # testing broken: './minc_wrapper: Permission denied' from Testing/ellipse0.mnc diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix index ad37a3a7dabf..2ba5964d6104 100644 --- a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "picard-tools-${version}"; - version = "2.18.20"; + version = "2.18.25"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "0dx6fxn6d7mawkah242fdi9wm8pdzmm4m004fb9ak2fsvrs2m5pk"; + sha256 = "03d3mnf3gddngn3dhwb00v8k40x6ncgprn22w4vyfr96917p2snx"; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix b/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix index 9c2d273b0881..dc2246903349 100644 --- a/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { name = "snpeff-${version}"; - version = "4.3q"; + version = "4.3t"; src = fetchurl { - url = "mirror://sourceforge/project/snpeff/snpEff_v4_3q_core.zip"; - sha256 = "0sxz8zy8wrzcy01hyb1cirwbxqyjw30a2x3q6p4l7zmw2szi7mn1"; + url = "mirror://sourceforge/project/snpeff/snpEff_v${builtins.replaceStrings [ "." ] [ "_" ] version}_core.zip"; + sha256 = "0i12mv93bfv8xjwc3rs2x73d6hkvi7kgbbbx3ry984l3ly4p6nnm"; }; buildInputs = [ unzip jre makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/biology/star/default.nix b/nixpkgs/pkgs/applications/science/biology/star/default.nix index cbe38649503b..4d1d60469f0e 100644 --- a/nixpkgs/pkgs/applications/science/biology/star/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/star/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { name = "star-${version}"; - version = "2.6.1d"; + version = "2.7.0a"; src = fetchFromGitHub { repo = "STAR"; owner = "alexdobin"; rev = version; - sha256 = "1h0j8qj95a0brv7p3gxmg3z7z6f4670jzjg56kzyc33k8dmzxvli"; + sha256 = "1yx28gra6gqdx1ps5y8mpdinsn8r0dhsc2m3gcvjfrk71i9yhd6l"; }; sourceRoot = "source/source"; |