diff options
Diffstat (limited to 'pkgs/applications/science/biology')
6 files changed, 167 insertions, 9 deletions
diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix new file mode 100644 index 000000000000..cd5c980b0016 --- /dev/null +++ b/pkgs/applications/science/biology/bedtools/default.nix @@ -0,0 +1,25 @@ +{stdenv, fetchFromGitHub, zlib, python}: + +stdenv.mkDerivation rec { + name = "bedtools-${version}"; + version = "2.26.0"; + + src = fetchFromGitHub { + owner = "arq5x"; + repo = "bedtools2"; + rev = "v${version}"; + sha256 = "1j2ia68rmcw3qksjm5gvv1cb84bh76vmln59mvncr2an23f5a3ss"; + }; + + buildInputs = [ zlib python ]; + buildPhase = "make prefix=$out SHELL=${stdenv.shell} -j $NIX_BUILD_CORES"; + installPhase = "make prefix=$out SHELL=${stdenv.shell} install"; + + meta = with stdenv.lib; { + description = "A powerful toolset for genome arithmetic."; + license = licenses.gpl2; + homepage = https://bedtools.readthedocs.io/en/latest/; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.unix; + }; +} diff --git a/pkgs/applications/science/biology/emboss/default.nix b/pkgs/applications/science/biology/emboss/default.nix index 331820276553..2110a9bcfaba 100644 --- a/pkgs/applications/science/biology/emboss/default.nix +++ b/pkgs/applications/science/biology/emboss/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchurl, readline, perl, libX11, libpng, libXt, zlib}: +{stdenv, fetchurl, readline, perl, libharu, libX11, libpng, libXt, zlib}: stdenv.mkDerivation { name = "emboss-6.6.0"; @@ -6,16 +6,14 @@ stdenv.mkDerivation { url = "ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz"; sha256 = "7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e"; }; - # patch = fetchurl { - # url = ftp://emboss.open-bio.org/pub/EMBOSS/fixes/patches/patch-1-9.gz; - # sha256 = "1pfn5zdxrr71c3kwpdkzmmsqvdwkmynkvcr707vqh73h9cjhk3c1"; - # }; - buildInputs = [readline perl libpng libX11 libXt zlib]; + buildInputs = [ readline perl libharu libpng libX11 libXt zlib ]; - # preConfigure = '' - # gzip -d $patch | patch -p1 - # ''; + configureFlags = [ "--with-hpdf=${libharu}" "--with-pngdriver=${zlib}" ]; + + postConfigure = '' + sed -i 's@$(bindir)/embossupdate@true@' Makefile + ''; meta = { description = "The European Molecular Biology Open Software Suite"; diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix new file mode 100644 index 000000000000..3f17825202ea --- /dev/null +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -0,0 +1,30 @@ +{stdenv, fetchurl, jre, makeWrapper}: + +stdenv.mkDerivation rec { + name = "picard-tools-${version}"; + version = "2.7.1"; + + src = fetchurl { + url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; + sha256 = "0rcfcvy9zacqmh7nyqlm93hzsx6gfygmcf8d2p02h5l69gvygnb9"; + }; + + buildInputs = [ jre makeWrapper ]; + + phases = [ "installPhase" ]; + + installPhase = '' + mkdir -p $out/libexec/picard + cp $src $out/libexec/picard/picard.jar + mkdir -p $out/bin + makeWrapper ${jre}/bin/java $out/bin/picard --add-flags "-jar $out/libexec/picard/picard.jar" + ''; + + meta = with stdenv.lib; { + description = "Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF."; + license = licenses.mit; + homepage = https://broadinstitute.github.io/picard/; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.all; + }; +} diff --git a/pkgs/applications/science/biology/platypus/default.nix b/pkgs/applications/science/biology/platypus/default.nix new file mode 100644 index 000000000000..868540fcbc3b --- /dev/null +++ b/pkgs/applications/science/biology/platypus/default.nix @@ -0,0 +1,38 @@ +{stdenv, fetchFromGitHub, python27, htslib, zlib, makeWrapper}: + +let python = python27.withPackages (ps: with ps; [ cython ]); + +in stdenv.mkDerivation rec { + name = "platypus-unstable-${version}"; + version = "2017-03-07"; + + src = fetchFromGitHub { + owner = "andyrimmer"; + repo = "Platypus"; + rev = "cbbd914"; + sha256 = "0xgj3pl7n4c12j5pp5qyjfk4rsvb5inwzrpcbhdf3br5f3mmdsb9"; + }; + + buildInputs = [ htslib python zlib makeWrapper ]; + + buildPhase = '' + patchShebangs . + make + ''; + + installPhase = '' + mkdir -p $out/libexec/platypus + cp -r ./* $out/libexec/platypus + + mkdir -p $out/bin + makeWrapper ${python}/bin/python $out/bin/platypus --add-flags "$out/libexec/platypus/bin/Platypus.py" + ''; + + meta = with stdenv.lib; { + description = "The Platypus variant caller"; + license = licenses.gpl3; + homepage = https://github.com/andyrimmer/Platypus; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.unix; + }; +} diff --git a/pkgs/applications/science/biology/snpeff/default.nix b/pkgs/applications/science/biology/snpeff/default.nix new file mode 100644 index 000000000000..6c7a6b969ee6 --- /dev/null +++ b/pkgs/applications/science/biology/snpeff/default.nix @@ -0,0 +1,31 @@ +{stdenv, fetchurl, jre, unzip, makeWrapper}: + +stdenv.mkDerivation rec { + name = "snpeff-${version}"; + version = "4.3i"; + + src = fetchurl { + url = "mirror://sourceforge/project/snpeff/snpEff_latest_core.zip"; + sha256 = "0i1slg201c8yjfr4wrg4xcgzwi0c8b9l3fb1i73fphq6q6zdblzb"; + }; + + buildInputs = [ unzip jre makeWrapper ]; + + installPhase = '' + mkdir -p $out/libexec/snpeff + cp *.jar *.config $out/libexec/snpeff + + mkdir -p $out/bin + makeWrapper ${jre}/bin/java $out/bin/snpeff --add-flags "-jar $out/libexec/snpeff/snpEff.jar" + makeWrapper ${jre}/bin/java $out/bin/snpsift --add-flags "-jar $out/libexec/snpeff/SnpSift.jar" + ''; + + meta = with stdenv.lib; { + description = "Genetic variant annotation and effect prediction toolbox."; + license = licenses.lgpl3; + homepage = http://snpeff.sourceforge.net/; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.all; + }; + +} diff --git a/pkgs/applications/science/biology/varscan/default.nix b/pkgs/applications/science/biology/varscan/default.nix new file mode 100644 index 000000000000..f685031e87e4 --- /dev/null +++ b/pkgs/applications/science/biology/varscan/default.nix @@ -0,0 +1,36 @@ +{stdenv, fetchurl, jre, makeWrapper}: + +stdenv.mkDerivation rec { + name = "varscan-${version}"; + version = "2.4.2"; + + src = fetchurl { + url = "https://github.com/dkoboldt/varscan/releases/download/${version}/VarScan.v${version}.jar"; + sha256 = "0cfhshinyqgwc6i7zf8lhbfybyly2x5anrz824zyvdhzz5i69zrl"; + }; + + buildInputs = [ jre makeWrapper ]; + + phases = [ "installPhase" ]; + + installPhase = '' + mkdir -p $out/libexec/varscan + cp $src $out/libexec/varscan/varscan.jar + mkdir -p $out/bin + makeWrapper ${jre}/bin/java $out/bin/varscan --add-flags "-jar $out/libexec/varscan/varscan.jar" + ''; + + meta = with stdenv.lib; { + description = "Variant calling and somatic mutation/CNV detection for next-generation sequencing data"; + # VarScan 2 is free for non-commercial use by academic, + # government, and non-profit/not-for-profit institutions. A + # commercial version of the software is available, and licensed + # through the Office of Technology Management at Washington + # University School of Medicine. + license = licenses.unfree; + homepage = https://github.com/dkoboldt/varscan; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.all; + }; + +} |