diff options
Diffstat (limited to 'infra/libkookie/nixpkgs/pkgs/applications/science/biology')
16 files changed, 48 insertions, 58 deletions
diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/ants/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/ants/default.nix index cb88e92fe1cb..ece218eea37d 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/ants/default.nix +++ b/infra/libkookie/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/infra/libkookie/nixpkgs/pkgs/applications/science/biology/bwa/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/bwa/default.nix index 7212b42198c4..10859d9e8c13 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/bwa/default.nix +++ b/infra/libkookie/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/infra/libkookie/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix index 59b173ac98cd..cfd1206f2314 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/infra/libkookie/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/infra/libkookie/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix index efa246a277fe..2621c5bbf037 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix +++ b/infra/libkookie/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 = "3.5.0"; - src = fetchPypi { - inherit pname version; - sha256 = "1a14a29e60be13eac11bd204dab9aef73cd72fe56a94c587333f21087584c0d8"; + 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/infra/libkookie/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix index 6ee7cd609c42..3b1420a18819 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix +++ b/infra/libkookie/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/infra/libkookie/nixpkgs/pkgs/applications/science/biology/igv/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/igv/default.nix index bc4f1677fc98..3f9cb1a288b3 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/igv/default.nix +++ b/infra/libkookie/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_${version}.zip"; - sha256 = "1874w1xprv91caz1ymfxilq6inhj36xzx8j9m0mcyp0qfvfvyjp7"; + sha256 = "0sab478jq96iw3fv0560hrrj8qbh40r8m4ncypdb7991j9haxl09"; }; installPhase = '' diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix index 5a1bb187886b..014ae14cc794 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = false; meta = with stdenv.lib; { - description = "Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data"; + description = "Program for quantifying abundances of transcripts from RNA-Seq data"; homepage = "https://pachterlab.github.io/kallisto"; license = licenses.bsd2; platforms = platforms.linux; diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/last/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/last/default.nix index 13f6a23913fc..0976e5a10802 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/last/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/last/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1066"; + version = "1145"; src = fetchurl { url = "http://last.cbrc.jp/last-${version}.zip"; - sha256 = "098j3f3a80rmhd01ds7rnb9y1xykmll2yh5ivpnvskssd8z2vc4r"; + sha256 = "0g54nmxxrirgid1i1k5i6rf7vnjpk9548sy06yqb4fj7vdzqgq99"; }; nativeBuildInputs = [ unzip ]; diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/lumpy/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/lumpy/default.nix index 04512e8e372e..f6267a2e017f 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/lumpy/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/lumpy/default.nix @@ -7,13 +7,14 @@ let in stdenv.mkDerivation rec { pname = "lumpy"; - version = "0.3.0"; + version = "0.3.1"; src = fetchFromGitHub { owner = "arq5x"; repo = "lumpy-sv"; - rev = version; - sha256 = "0azhzvmh9az9jcq0xprlzdz6w16azgszv4kshb903bwbnqirmk18"; + rev = "v${version}"; + sha256 = "0r71sg7qch8r6p6dw995znrqdj6q49hjdylhzbib2qmv8nvglhs9"; + fetchSubmodules = true; }; nativeBuildInputs = [ which ]; @@ -26,6 +27,8 @@ in stdenv.mkDerivation rec { # Use Nix htslib over bundled version sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile + # Also make sure we use the includes from Nix's htslib + sed -i 's|../../lib/htslib/|${htslib}|' src/filter/Makefile ''; # Upstream's makefile doesn't have an install target diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix index d0f98719fa1a..d2b05943f7ce 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix +++ b/infra/libkookie/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${version}"; - sha256 = "01gm9gj2x2zs4yx6wk761fi1papi7qr3gp4ln1kkn8n2f9y9h849"; + sha256 = "1kcrvamrafz1m0s7mlbhaay8jyg97l1w37p6syl36r2m1plmwxjd"; }; nativeBuildInputs = [ nim ]; diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix index d496e78748d9..0353f2e7cebd 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "2.23.4"; + version = "2.23.8"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "0xg4nbx02a2kckr6p8pqjpv5rmp95bkmglgm1bma6f77s7hkab7q"; + sha256 = "0aflbsxzc2pcp195bbgwk6zqabq0pszc41s1pw17khn8ywl2jjr2"; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/plink/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/plink/default.nix deleted file mode 100644 index 009e12aa02f0..000000000000 --- a/infra/libkookie/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 $out/bin - ''; - - meta = { - description = "Whole genome association toolkit"; - homepage = "http://pngu.mgh.harvard.edu/~purcell/plink/"; - license = stdenv.lib.licenses.gpl2; - platforms = stdenv.lib.platforms.all; - broken = true; - }; -} diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix index 7795ba237367..6846e3c84fae 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix +++ b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samblaster/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "samblaster"; - version = "0.1.24"; + version = "0.1.26"; src = fetchFromGitHub { owner = "GregoryFaust"; repo = "samblaster"; rev = "v.${version}"; - sha256 = "0iv2ddfw8363vb2x8gr3p8g88whb6mb9m0pf71i2cqsbv6jghap7"; + sha256 = "0g24fq5hplnfgqkh3xqpg3lgx3wmxwnh9c7m6yw7pbi40lmgl1jv"; }; installPhase = '' diff --git a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samtools/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samtools/default.nix index e750eea89ac9..27ed79a1f6ca 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/samtools/default.nix +++ b/infra/libkookie/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/infra/libkookie/nixpkgs/pkgs/applications/science/biology/star/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/star/default.nix index c331acbfe705..f2e1a2a8fee5 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/star/default.nix +++ b/infra/libkookie/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/infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix b/infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix index 07669d097a44..82c624ba7cd9 100644 --- a/infra/libkookie/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix +++ b/infra/libkookie/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"; |