diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology')
7 files changed, 104 insertions, 2 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix b/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix index dbcfead6b1e..696162d2dc5 100644 --- a/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix @@ -26,5 +26,6 @@ stdenv.mkDerivation rec { pname = "EZminc"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; license = licenses.free; + broken = true; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/delly/default.nix b/nixpkgs/pkgs/applications/science/biology/delly/default.nix new file mode 100644 index 00000000000..bfdf5a1bb17 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/delly/default.nix @@ -0,0 +1,40 @@ +{ stdenv, fetchFromGitHub, htslib, zlib, bzip2, lzma, ncurses, boost }: + +stdenv.mkDerivation rec { + pname = "delly"; + version = "0.8.1"; + + src = fetchFromGitHub { + owner = "dellytools"; + repo = pname; + rev = "v${version}"; + sha256 = "18gm86j1g1k4z1cjv2m5v9rsl1xqs2w3dhwcsnzx2mhkrvmlc4i1"; + }; + + buildInputs = [ zlib htslib bzip2 lzma ncurses boost ]; + + EBROOTHTSLIB = htslib; + + installPhase = '' + runHook preInstall + + install -Dm555 src/delly $out/bin/delly + + runHook postInstall + ''; + + meta = with stdenv.lib; { + description = "Structural variant caller for mapped DNA sequenced data"; + license = licenses.gpl3; + maintainers = with maintainers; [ scalavision ]; + platforms = platforms.linux; + longDescription = '' + Delly is an integrated structural variant (SV) prediction method + that can discover, genotype and visualize deletions, tandem duplications, + inversions and translocations at single-nucleotide resolution in + short-read massively parallel sequencing data. It uses paired-ends, + split-reads and read-depth to sensitively and accurately delineate + genomic rearrangements throughout the genome. + ''; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/macse/default.nix b/nixpkgs/pkgs/applications/science/biology/macse/default.nix new file mode 100644 index 00000000000..59938addbe8 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/macse/default.nix @@ -0,0 +1,32 @@ +{ stdenv, fetchurl, jre, makeWrapper }: + +stdenv.mkDerivation rec { + pname = "macse"; + version = "2.03"; + + src = fetchurl { + url = "https://bioweb.supagro.inra.fr/${pname}/releases/${pname}_v${version}.jar"; + sha256 = "0jnjyz4f255glg37rawzdv4m6nfs7wfwc5dny7afvx4dz2sv4ssh"; + }; + + nativeBuildInputs = [ makeWrapper ]; + + dontBuild = true; + unpackPhase = ":"; + + installPhase = '' + runHook preInstall + mkdir -p $out/share/java + cp -s $src $out/share/java/macse.jar + makeWrapper ${jre}/bin/java $out/bin/macse --add-flags "-jar $out/share/java/macse.jar" + runHook postInstall + ''; + + meta = with stdenv.lib; { + description = "Multiple alignment of coding sequences"; + homepage = "https://bioweb.supagro.inra.fr/macse/"; + license = licenses.gpl2; + maintainers = [ maintainers.bzizou ]; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/paml/default.nix b/nixpkgs/pkgs/applications/science/biology/paml/default.nix index 161188f7ef1..fe6919656d9 100644 --- a/nixpkgs/pkgs/applications/science/biology/paml/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/paml/default.nix @@ -29,5 +29,6 @@ stdenv.mkDerivation rec { longDescription = ''PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.''; license = "non-commercial"; homepage = http://abacus.gene.ucl.ac.uk/software/paml.html; + broken = true; }; } diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix index 2a57febe8f5..8fff296affa 100644 --- a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.20.5"; + version = "2.20.8"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "107zlvp74ahpn652nfkipp80bbzf3fp812pi1ma42njk4wchah10"; + sha256 = "01bibkwyp4xzwcpvkr3ab6z0syjmzj4zmyxl3bybmrp9irhjvydg"; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/biology/spades/default.nix b/nixpkgs/pkgs/applications/science/biology/spades/default.nix new file mode 100644 index 00000000000..a195f79010a --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/spades/default.nix @@ -0,0 +1,27 @@ +{ stdenv, fetchurl, zlib, bzip2, cmake }: + +stdenv.mkDerivation rec { + pname = "SPAdes"; + version = "3.13.1"; + + src = fetchurl { + url = "http://cab.spbu.ru/files/release${version}/${pname}-${version}.tar.gz"; + sha256 = "0giayz197lmq2108filkn9izma3i803sb3iskv9hs5snzdr9p8ld"; + }; + + nativeBuildInputs = [ cmake ]; + + buildInputs = [ zlib bzip2 ]; + + doCheck = true; + + sourceRoot = "${pname}-${version}/src"; + + meta = with stdenv.lib; { + description = "St. Petersburg genome assembler: assembly toolkit containing various assembly pipelines"; + license = licenses.gpl2; + homepage = "http://cab.spbu.ru/software/spades/"; + platforms = platforms.unix; + maintainers = [ maintainers.bzizou ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/strelka/default.nix b/nixpkgs/pkgs/applications/science/biology/strelka/default.nix index 84c90d89556..c791e8ef89b 100644 --- a/nixpkgs/pkgs/applications/science/biology/strelka/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/strelka/default.nix @@ -33,6 +33,7 @@ stdenv.mkDerivation rec { homepage = https://github.com/Illumina/strelka; maintainers = with maintainers; [ jbedo ]; platforms = [ "x86_64-linux" ]; + broken = true; }; } |