diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology')
30 files changed, 955 insertions, 40 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix b/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix index dbcfead6b1ea..978615fa4592 100644 --- a/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix @@ -1,16 +1,17 @@ -{ stdenv, fetchFromGitHub, cmake, libminc, bicpl, itk, fftwFloat, gsl }: +{ stdenv, fetchFromGitHub, cmake, pkgconfig, libminc, bicpl, itk, fftwFloat, gsl }: -stdenv.mkDerivation rec { pname = "EZminc"; - name = "${pname}-2017-08-29"; +stdenv.mkDerivation rec { + pname = "EZminc"; + name = "${pname}-unstable-2019-07-25"; src = fetchFromGitHub { owner = "BIC-MNI"; repo = pname; - rev = "4e017236cb6e7f6e07507446b18b759c584b6fc3"; - sha256 = "1pg06x42pgsg7zy7dz9wf6ajakkm2n8by64lg9z64qi8qqy82b8v"; + rev = "9591edd5389a5bda2c1f606816c7cdb35c065adf"; + sha256 = "02k87qbpx0f48l2lbcjmlqx82py684z3sfi29va5icfg3hjd6j7b"; }; - nativeBuildInputs = [ cmake ]; + nativeBuildInputs = [ cmake pkgconfig ]; buildInputs = [ itk libminc bicpl fftwFloat gsl ]; cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" diff --git a/nixpkgs/pkgs/applications/science/biology/bayescan/default.nix b/nixpkgs/pkgs/applications/science/biology/bayescan/default.nix new file mode 100644 index 000000000000..4e216fbdbe63 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/bayescan/default.nix @@ -0,0 +1,39 @@ +{ stdenv, fetchurl, unzip, llvmPackages }: + +stdenv.mkDerivation rec { + pname = "bayescan"; + version = "2.1"; + + src = fetchurl { + url = "http://cmpg.unibe.ch/software/BayeScan/files/BayeScan${version}.zip"; + sha256 = "0ismima8j8z0zj9yc267rpf7z90w57b2pbqzjnayhc3ab8mcbfy6"; + }; + + nativeBuildInputs = [ unzip ]; + buildInputs = stdenv.lib.optional stdenv.cc.isClang llvmPackages.openmp; + + # Disable FORTIFY_SOURCE or the binary fails with "buffer overflow" + hardeningDisable = [ "fortify" ]; + + sourceRoot = "BayeScan${version}/source"; + + postPatch = '' + substituteInPlace Makefile --replace "-static" "" \ + --replace "g++" "c++" + ''; + + installPhase = '' + mkdir -p $out/bin + mkdir -p $out/share/doc/bayescan + cp bayescan_${version} $out/bin + cp -r ../*pdf ../input_examples ../"R functions" $out/share/doc/bayescan + ''; + + meta = with stdenv.lib; { + description = "Detecting natural selection from population-based genetic data"; + homepage = "http://cmpg.unibe.ch/software/BayeScan"; + license = licenses.gpl3; + maintainers = [ maintainers.bzizou ]; + platforms = stdenv.lib.platforms.all; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix b/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix index 33e4de0d95aa..4a6a464de464 100644 --- a/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "bcftools"; - version = "1.9"; + version = "1.10.2"; src = fetchurl { url = "https://github.com/samtools/bcftools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg"; + sha256 = "0b2f6lqhxdlrvfjqxv7a4nzqj68c1j4avn16iqxwwm80kn302wzm"; }; 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 4e4c093ad7f7..9af2ec88c392 100644 --- a/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix @@ -2,19 +2,20 @@ stdenv.mkDerivation rec { pname = "bedtools"; - version = "2.29.0"; + version = "2.29.2"; src = fetchFromGitHub { owner = "arq5x"; repo = "bedtools2"; rev = "v${version}"; - sha256 = "0d6i985qqxp92ddq4n6558m70qi5rqhl724wrfys0hm0p6a9h56x"; + sha256 = "015qq3pwrwgnyxyi959niijjlswl231b3wxlsm3l8msv6fdhmkz8"; }; buildInputs = [ zlib python bzip2 lzma ]; - cc = if stdenv.cc.isClang then "clang++" else "g++"; - buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} -j $NIX_BUILD_CORES"; - installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} install"; + cxx = if stdenv.cc.isClang then "clang++" else "g++"; + cc = if stdenv.cc.isClang then "clang" else "gcc"; + buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} -j $NIX_BUILD_CORES"; + installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} install"; meta = with stdenv.lib; { description = "A powerful toolset for genome arithmetic."; diff --git a/nixpkgs/pkgs/applications/science/biology/bftools/default.nix b/nixpkgs/pkgs/applications/science/biology/bftools/default.nix index 158291049347..29e8bca52625 100644 --- a/nixpkgs/pkgs/applications/science/biology/bftools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bftools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "bftools"; - version = "5.9.2"; + version = "6.3.0"; src = fetchzip { url = "http://downloads.openmicroscopy.org/bio-formats/${version}/artifacts/bftools.zip"; - sha256 = "08lmbg3kfxh17q6548il0i2h3f9a6ch8r0r067p14dajhzfpjyqj"; + sha256 = "02nvvmpfglpah1ihd08aw65g1794w588c988cdar1hfl4s80qwhb"; }; installPhase = '' diff --git a/nixpkgs/pkgs/applications/science/biology/blast/default.nix b/nixpkgs/pkgs/applications/science/biology/blast/default.nix new file mode 100644 index 000000000000..ad737c6699d6 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/blast/default.nix @@ -0,0 +1,108 @@ +{ lib, stdenv, fetchurl, zlib, bzip2, perl, cpio, gawk, coreutils, ApplicationServices }: + +stdenv.mkDerivation rec { + pname = "blast"; + version = "2.10.0"; + + src = fetchurl { + url = "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-src.tar.gz"; + sha256 = "09nry5knj5hhxpn0a5ww1gb1704grd4r1y7adbjl6kqwq37dkk9s"; + }; + + sourceRoot = "ncbi-blast-${version}+-src/c++"; + + configureFlags = [ + # With flat Makefile we can use all_projects in order not to build extra. + # These extra cause clang to hang on Darwin. + "--with-flat-makefile" + "--without-makefile-auto-update" + "--with-dll" # build dynamic libraries (static are default) + ]; + + makeFlags = [ "all_projects=app/" ]; + + preConfigure = '' + export NCBICXX_RECONF_POLICY=warn + export PWD=$(pwd) + export HOME=$PWD + + # The configure scripts wants to set AR="ar cr" unless it is already set in + # the environment. Because stdenv sets AR="ar", the result is a bad call to + # the assembler later in the process. Thus, we need to unset AR + unset AR + + for awks in scripts/common/impl/is_log_interesting.awk \ + scripts/common/impl/report_duplicates.awk; do + + substituteInPlace $awks \ + --replace /usr/bin/awk ${gawk}/bin/awk + done + + for mk in src/build-system/Makefile.meta.in \ + src/build-system/helpers/run_with_lock.c ; do + + substituteInPlace $mk \ + --replace /bin/rm ${coreutils}/bin/rm + done + + for mk in src/build-system/Makefile.meta.gmake=no \ + src/build-system/Makefile.meta_l \ + src/build-system/Makefile.meta_r \ + src/build-system/Makefile.requirements \ + src/build-system/Makefile.rules_with_autodep.in; do + + substituteInPlace $mk \ + --replace /bin/echo ${coreutils}/bin/echo + done + for mk in src/build-system/Makefile.meta_p \ + src/build-system/Makefile.rules_with_autodep.in \ + src/build-system/Makefile.protobuf.in ; do + + substituteInPlace $mk \ + --replace /bin/mv ${coreutils}/bin/mv + done + + + substituteInPlace src/build-system/configure \ + --replace /bin/pwd ${coreutils}/bin/pwd \ + --replace /bin/ln ${coreutils}/bin/ln + + substituteInPlace src/build-system/configure.ac \ + --replace /bin/pwd ${coreutils}/bin/pwd \ + --replace /bin/ln ${coreutils}/bin/ln + + substituteInPlace src/build-system/Makefile.meta_l \ + --replace /bin/date ${coreutils}/bin/date + ''; + + nativeBuildInputs = [ perl ]; + + # perl is necessary in buildInputs so that installed perl scripts get patched + # correctly + buildInputs = [ coreutils perl gawk zlib bzip2 cpio ] + ++ lib.optionals stdenv.isDarwin [ ApplicationServices ]; + hardeningDisable = [ "format" ]; + + postInstall = '' + substituteInPlace $out/bin/get_species_taxids.sh \ + --replace /bin/rm ${coreutils}/bin/rm + ''; + patches = [ ./no_slash_bin.patch ]; + + enableParallelBuilding = true; + + # Many tests require either network access or locally available databases + doCheck = false; + + meta = with stdenv.lib; { + description = ''Basic Local Alignment Search Tool (BLAST) finds regions of + similarity between biological sequences''; + homepage = https://blast.ncbi.nlm.nih.gov/Blast.cgi; + license = licenses.publicDomain; + + # Version 2.10.0 fails on Darwin + # See https://github.com/NixOS/nixpkgs/pull/61430 + platforms = platforms.linux; + maintainers = with maintainers; [ luispedro ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/blast/no_slash_bin.patch b/nixpkgs/pkgs/applications/science/biology/blast/no_slash_bin.patch new file mode 100644 index 000000000000..9b78ac579264 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/blast/no_slash_bin.patch @@ -0,0 +1,184 @@ +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/collect_outside_libs.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/collect_outside_libs.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/collect_outside_libs.sh 2014-08-01 22:01:17.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/collect_outside_libs.sh 2019-05-15 12:40:44.145239480 +0800 +@@ -1,8 +1,5 @@ + #!/bin/sh + set -e +-PATH=/bin:/usr/bin +-export PATH +-unset CDPATH + + base=$1 + search=`echo ${2-$LD_LIBRARY_PATH} | tr : ' '` +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/create_flat_tuneups.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/create_flat_tuneups.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/create_flat_tuneups.sh 2011-08-17 02:55:10.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/create_flat_tuneups.sh 2019-05-15 12:40:48.449276574 +0800 +@@ -1,9 +1,6 @@ + #!/bin/sh + id='$Id: create_flat_tuneups.sh 331412 2011-08-16 18:55:10Z ucko $' + +-PATH=/bin:/usr/bin +-export PATH +- + exec > auto_flat_tuneups.mk + + cat <<EOF +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/get_lock.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/get_lock.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/get_lock.sh 2011-08-20 04:12:28.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/get_lock.sh 2019-05-15 12:40:52.901315000 +0800 +@@ -1,7 +1,5 @@ + #!/bin/sh + +-PATH=/bin:/usr/bin +-export PATH + + dir=$1.lock + +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/if_diff.sh 2014-07-30 22:06:45.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/if_diff.sh 2019-05-15 12:42:57.298410841 +0800 +@@ -4,9 +4,6 @@ + # Author: Denis Vakatov (vakatov@ncbi.nlm.nih.gov) + ################################# + +-orig_PATH=$PATH +-PATH=/bin:/usr/bin +- + script_name=`basename $0` + script_args="$*" + +@@ -16,7 +13,7 @@ + base_action=`basename "$action"` + case "$base_action" in + cp | cp\ * | ln | ln\ * ) +- action=/bin/$base_action ++ action=$base_action + rm="rm -f" + ;; + * ) +@@ -58,10 +55,8 @@ + shift + cmd="$* $dest_file" + test "$quiet" = yes || echo "$cmd" +- PATH=$orig_PATH + "$@" "$dest" + status=$? +- PATH=/bin:/usr/bin + return $status + } + +@@ -74,7 +69,7 @@ + case "$base_action" in + ln | ln\ -f ) + test "$quiet" = yes || echo "failed; trying \"cp -p ...\" instead" +- cmd="/bin/cp -p $src_file $dest_file" ++ cmd="cp -p $src_file $dest_file" + ExecHelper "$dest_file" /bin/cp -p "$src_file" || + Usage "\"$cmd\" failed" + ;; +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/make_lock_map.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/make_lock_map.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/make_lock_map.sh 2011-11-17 04:43:52.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/make_lock_map.sh 2019-05-15 12:40:56.769348434 +0800 +@@ -1,8 +1,6 @@ + #!/bin/sh + # $Id: make_lock_map.sh 344587 2011-11-16 20:43:52Z ucko $ + +-PATH=/bin:/usr/bin +-export PATH + + act=false + cache_dir='.#SRC-cache' +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/run_with_lock.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/run_with_lock.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/run_with_lock.sh 2015-10-29 22:36:05.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/run_with_lock.sh 2019-05-15 12:41:53.401842849 +0800 +@@ -1,10 +1,6 @@ + #!/bin/sh + # $Id: run_with_lock.sh 483249 2015-10-29 14:36:05Z ucko $ + +-orig_PATH=$PATH +-PATH=/bin:/usr/bin +-export PATH +- + base= + logfile= + map= +@@ -23,7 +19,7 @@ + : ${base:=`basename "$1"`} + + clean_up () { +- /bin/rm -rf "$base.lock" ++ rm -rf "$base.lock" + } + + case $0 in +@@ -45,7 +41,7 @@ + trap "clean_up; exit $error_status" 1 2 15 + if [ -n "$logfile" ]; then + status_file=$base.lock/status +- (PATH=$orig_PATH; export PATH; "$@"; echo $? > "$status_file") 2>&1 \ ++ ("$@"; echo $? > "$status_file") 2>&1 \ + | tee "$logfile.new" + # Emulate egrep -q to avoid having to move from under scripts. + if [ ! -f "$logfile" ] \ +@@ -58,8 +54,6 @@ + status=1 + fi + else +- PATH=$orig_PATH +- export PATH + "$@" + status=$? + fi +diff -u --recursive ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.sh ncbi-blast-2.9.0+-src.patched/scripts/common/impl/strip_for_install.sh +--- ncbi-blast-2.9.0+-src/scripts/common/impl/strip_for_install.sh 2013-09-24 03:06:51.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/strip_for_install.sh 2019-05-15 12:40:13.272975092 +0800 +@@ -1,8 +1,5 @@ + #!/bin/sh + +-PATH=/bin:/usr/bin:/usr/ccs/bin +-export PATH +- + case "$1" in + --dirs ) + shift +--- ncbi-blast-2.9.0+-src/scripts/common/impl/update_configurable.sh 2017-07-13 22:53:24.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/scripts/common/impl/update_configurable.sh 2019-05-15 15:03:35.861276083 +0800 +@@ -1,6 +1,4 @@ + #!/bin/sh +-PATH=/bin:/usr/bin +-export PATH + + script_name=`basename $0` + script_dir=`dirname $0` +--- ncbi-blast-2.9.0+-src/src/build-system/Makefile.mk.in 2019-01-04 01:38:37.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/src/build-system/Makefile.mk.in 2019-05-15 15:14:41.749416495 +0800 +@@ -50,12 +50,12 @@ + + ### Auxiliary commands, filters + +-RM = /bin/rm -f +-RMDIR = /bin/rm -rf +-COPY = /bin/cp -p ++RM = rm -f ++RMDIR = rm -rf ++COPY = cp -p + BINCOPY = @BINCOPY@ + TOUCH = @TOUCH@ +-MKDIR = /bin/mkdir ++MKDIR = mkdir + BINTOUCH = $(TOUCH) + LN_S = @LN_S@ + GREP = @GREP@ +--- ncbi-blast-2.9.0+-src/src/build-system/configure 2019-03-05 00:49:08.000000000 +0800 ++++ ncbi-blast-2.9.0+-src.patched/src/build-system/configure 2019-05-15 16:55:40.711795042 +0800 +@@ -10417,10 +10417,6 @@ + echo "${ECHO_T}no, using $LN_S" >&6; } + fi + +-case "$LN_S" in +- /*) ;; +- * ) LN_S=/bin/$LN_S ;; +-esac + + if test -n "$ac_tool_prefix"; then + # Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args. diff --git a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix index 63d51de9930f..7c328034a306 100644 --- a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix @@ -6,14 +6,14 @@ }: stdenv.mkDerivation rec { - version = "1.0.20190410"; + version = "1.0.20190902"; pname = "dcm2niix"; src = fetchFromGitHub { owner = "rordenlab"; repo = "dcm2niix"; rev = "v${version}"; - sha256 = "1prwpvbi76xlpkhc4kadjhyyx0s71cs30hi6anknhfm6hdyd26ms"; + sha256 = "0h8jsadgv831lqb0jhnaxm7lldirmnp5agrhgg5bcxvn860fl15b"; }; enableParallelBuilding = true; diff --git a/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix b/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix new file mode 100644 index 000000000000..78a6f483337f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix @@ -0,0 +1,42 @@ +{ lib +, python +}: +with python.pkgs; +buildPythonApplication rec { + pname = "deepTools"; + version = "3.3.1"; + + src = fetchPypi { + inherit pname version; + sha256 = "08p36p9ncj5s8qf1r7h83x4rnmi63l3yk6mnr3wgpg2qgvwl0hji"; + }; + + propagatedBuildInputs = [ + numpy + numpydoc + scipy + py2bit + pybigwig + pysam + matplotlib + plotly + deeptoolsintervals + ]; + + checkInputs = [ pytest ]; + + meta = with lib; { + homepage = "https://deeptools.readthedocs.io/en/develop"; + description = "Tools for exploring deep DNA sequencing data"; + longDescription = '' + deepTools contains useful modules to process the mapped reads data for multiple + quality checks, creating normalized coverage files in standard bedGraph and bigWig + file formats, that allow comparison between different files (for example, treatment and control). + Finally, using such normalized and standardized files, deepTools can create many + publication-ready visualizations to identify enrichments and for functional + annotations of the genome. + ''; + license = licenses.gpl3; + maintainers = with maintainers; [ scalavision ]; + }; +} 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 000000000000..bfdf5a1bb17e --- /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 $out/bin/delly + + runHook postInstall + ''; + + meta = with stdenv.lib; { + description = "Structural variant caller for mapped DNA sequenced data"; + license = licenses.gpl3; + maintainers = with maintainers; [ scalavision ]; + platforms = platforms.linux; + longDescription = '' + Delly is an integrated structural variant (SV) prediction method + that can discover, genotype and visualize deletions, tandem duplications, + inversions and translocations at single-nucleotide resolution in + short-read massively parallel sequencing data. It uses paired-ends, + split-reads and read-depth to sensitively and accurately delineate + genomic rearrangements throughout the genome. + ''; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix b/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix index e1e84c9423bb..7d0a36e755f6 100644 --- a/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix @@ -2,14 +2,14 @@ stdenv.mkDerivation rec { pname = "freebayes"; - version = "2017-08-23"; + version = "1.3.1"; src = fetchFromGitHub { name = "freebayes-${version}-src"; owner = "ekg"; repo = "freebayes"; - rev = "8d2b3a060da473e1f4f89be04edfce5cba63f1d3"; - sha256 = "0yyrgk2639lz1yvg4jf0ccahnkic31dy77q05pb3i28rjf37v45z"; + rev = "v${version}"; + sha256 = "035nriknjqq8gvil81vvsmvqwi35v80q8h1cw24vd1gdyn1x7bys"; fetchSubmodules = true; }; diff --git a/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix b/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix index 3adbaf0079ef..69ecb228697b 100644 --- a/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix @@ -1,12 +1,12 @@ { stdenv, fetchurl }: stdenv.mkDerivation rec { - version = "3.2.1"; + version = "3.3"; pname = "hmmer"; src = fetchurl { url = "http://eddylab.org/software/hmmer/${pname}-${version}.tar.gz"; - sha256 = "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5"; + sha256 = "0v3kcgkr6jihq0xmpgn2xd5q7wiwvj6yswa905k2c0v7mx0bz1h1"; }; meta = with stdenv.lib; { diff --git a/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix b/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix index de93ae5d7829..1a6555e0d634 100644 --- a/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "kallisto"; - version = "0.46.0"; + version = "0.46.1"; src = fetchFromGitHub { repo = "kallisto"; owner = "pachterlab"; rev = "v${version}"; - sha256 = "09vgdqwpigl4x3sdw5vjfyknsllkli339mh8xapbf7ldm0jldfn9"; + sha256 = "09ldgy70wziw51ma4a3b7vyrphzf2v1cnq1j5r1wwgfmx8fgbh2z"; }; nativeBuildInputs = [ autoconf cmake ]; diff --git a/nixpkgs/pkgs/applications/science/biology/kssd/default.nix b/nixpkgs/pkgs/applications/science/biology/kssd/default.nix new file mode 100644 index 000000000000..ef8a0ce136f8 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/kssd/default.nix @@ -0,0 +1,25 @@ +{ stdenv, fetchurl, zlib, automake, autoconf, libtool }: + +stdenv.mkDerivation rec { + pname = "kssd"; + version = "1.0"; + + src = fetchurl { + url = "https://github.com/yhg926/public_${pname}/archive/v${version}.tar.gz"; + sha256 = "a5dcaf520049a962bef625cb59a567ea2b4252d4dc9be28dd06123d340e03919"; + }; + + buildInputs = [ zlib automake autoconf libtool ]; + + installPhase = '' + install -vD kssd $out/bin/kssd + ''; + + meta = with stdenv.lib; { + description = "K-mer substring space decomposition"; + license = licenses.asl20; + homepage = "https://github.com/yhg926/public_kssd"; + maintainers = with maintainers; [ unode ]; + platforms = [ "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/last/default.nix b/nixpkgs/pkgs/applications/science/biology/last/default.nix new file mode 100644 index 000000000000..c9e546dc2ce7 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/last/default.nix @@ -0,0 +1,30 @@ +{ stdenv, fetchurl, unzip, zlib, python3, parallel }: + +stdenv.mkDerivation rec { + pname = "last"; + version = "1045"; + + src = fetchurl { + url = "http://last.cbrc.jp/last-${version}.zip"; + sha256 = "0x2wrm52ca935n3yc486m8yy59ap34w1x9h3csjca3jab5agnjkc"; + }; + + nativeBuildInputs = [ unzip ]; + buildInputs = [ zlib python3 ]; + + makeFlags = [ "prefix=${placeholder "out"}" ]; + + postFixup = '' + for f in $out/bin/parallel-* ; do + sed -i 's|parallel |${parallel}/bin/parallel |' $f + done + ''; + + meta = with stdenv.lib; { + description = "Genomic sequence aligner"; + homepage = "http://last.cbrc.jp/"; + license = licenses.gpl3; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.x86_64; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/macse/default.nix b/nixpkgs/pkgs/applications/science/biology/macse/default.nix new file mode 100644 index 000000000000..59938addbe82 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/macse/default.nix @@ -0,0 +1,32 @@ +{ stdenv, fetchurl, jre, makeWrapper }: + +stdenv.mkDerivation rec { + pname = "macse"; + version = "2.03"; + + src = fetchurl { + url = "https://bioweb.supagro.inra.fr/${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 $out/share/java/macse.jar" + runHook postInstall + ''; + + meta = with stdenv.lib; { + description = "Multiple alignment of coding sequences"; + homepage = "https://bioweb.supagro.inra.fr/macse/"; + license = licenses.gpl2; + maintainers = [ maintainers.bzizou ]; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/megahit/default.nix b/nixpkgs/pkgs/applications/science/biology/megahit/default.nix index 56bb35b64df8..86414980177f 100644 --- a/nixpkgs/pkgs/applications/science/biology/megahit/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/megahit/default.nix @@ -1,23 +1,20 @@ -{ stdenv, fetchFromGitHub, zlib }: +{ stdenv, fetchFromGitHub, cmake, zlib }: stdenv.mkDerivation rec { pname = "megahit"; - version = "1.1.4"; + version = "1.2.9"; src = fetchFromGitHub { owner = "voutcn"; repo = "megahit"; rev = "v${version}"; - sha256 = "011k0776w76l03zmy70kfd3y9zjmdnspfbs9fcxmnl3bdwd36kcw"; + sha256 = "1r5d9nkdmgjsbrpj43q9hy3s8jwsabaz3ji561v18hy47v58923c"; }; + nativeBuildInputs = [ cmake ]; buildInputs = [ zlib ]; - installPhase = '' - for bin in megahit_sdbg_build megahit megahit_asm_core megahit_toolkit; do - install -vD $bin $out/bin/$bin - done - ''; + enableParallelBuilding = true; meta = with stdenv.lib; { description = "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph"; diff --git a/nixpkgs/pkgs/applications/science/biology/minia/default.nix b/nixpkgs/pkgs/applications/science/biology/minia/default.nix new file mode 100644 index 000000000000..2a80de733b08 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/minia/default.nix @@ -0,0 +1,33 @@ +{ stdenv, fetchFromGitHub, cmake, hdf5, boost }: + +stdenv.mkDerivation rec { + pname = "minia"; + version = "3.2.1"; + + src = fetchFromGitHub { + owner = "GATB"; + repo = "minia"; + rev = "v${version}"; + sha256 = "0bmfrywixaaql898l0ixsfkhxjf2hb08ssnqzlzacfizxdp46siq"; + fetchSubmodules = true; + }; + + patches = [ ./no-bundle.patch ]; + + NIX_CFLAGS_COMPILE = [ "-Wformat" ]; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ hdf5 boost ]; + + prePatch = '' + rm -rf thirdparty/gatb-core/gatb-core/thirdparty/{hdf5,boost} + ''; + + meta = with stdenv.lib; { + description = "Short read genome assembler"; + homepage = "https://github.com/GATB/minia"; + license = licenses.agpl3; + maintainers = with maintainers; [ jbedo ]; + platforms = [ "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/minia/no-bundle.patch b/nixpkgs/pkgs/applications/science/biology/minia/no-bundle.patch new file mode 100644 index 000000000000..21d12c7f6f2d --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/minia/no-bundle.patch @@ -0,0 +1,222 @@ +diff --git a/thirdparty/gatb-core/gatb-core/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/CMakeLists.txt +index f48a70b..0e11ece 100644 +--- a/thirdparty/gatb-core/gatb-core/CMakeLists.txt ++++ b/thirdparty/gatb-core/gatb-core/CMakeLists.txt +@@ -257,7 +257,6 @@ ADD_SUBDIRECTORY(thirdparty) + # DEPENDENCIES + ################################################################################ + # we must be sure that hdf5 is built and installed before building gatb-core +-ADD_DEPENDENCIES (gatbcore-static hdf5 hdf5_postbuild) + + ################################################################################ + # DOCUMENTATION GENERATION +@@ -288,7 +287,6 @@ IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE) + INSTALL (FILES ${PROJECT_SOURCE_DIR}/doc/misc/README.txt DESTINATION . OPTIONAL) + INSTALL (FILES ${PROJECT_SOURCE_DIR}/LICENCE DESTINATION . OPTIONAL) + INSTALL (FILES ${PROJECT_SOURCE_DIR}/THIRDPARTIES.md DESTINATION . OPTIONAL) +- INSTALL (DIRECTORY ${PROJECT_SOURCE_DIR}/thirdparty/boost DESTINATION ./include) + ENDIF() + + ################################################################################ +diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp +index dfeee1c..d5553a2 100644 +--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp ++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/LargeInt.hpp +@@ -35,7 +35,7 @@ + #include <stdint.h> + #include <algorithm> + #include <iostream> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + #include <gatb/system/api/Exception.hpp> + #include <gatb/system/api/config.hpp> +diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp +index 60be5d5..25ae75e 100644 +--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp ++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt128.hpp +@@ -33,7 +33,7 @@ + /********************************************************************************/ + + #include <iostream> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + #include <gatb/system/api/types.hpp> + #include <gatb/tools/misc/api/Abundance.hpp> +diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp +index 6a71bb0..b9205df 100644 +--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp ++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt16.hpp +@@ -31,7 +31,7 @@ + #include <iostream> + #include <gatb/system/api/types.hpp> + #include <gatb/tools/misc/api/Abundance.hpp> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + /********************************************************************************/ + namespace gatb { +diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp +index c22b892..62e6586 100644 +--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp ++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt32.hpp +@@ -31,7 +31,7 @@ + #include <iostream> + #include <gatb/system/api/types.hpp> + #include <gatb/tools/misc/api/Abundance.hpp> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + /********************************************************************************/ + namespace gatb { +diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp +index c06aaab..e0befba 100644 +--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp ++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt64.hpp +@@ -31,7 +31,7 @@ + #include <iostream> + #include <gatb/system/api/types.hpp> + #include <gatb/tools/misc/api/Abundance.hpp> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + extern const unsigned char revcomp_4NT[]; + extern const unsigned char comp_NT []; +diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp +index 9659874..0c79ff6 100644 +--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp ++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/math/NativeInt8.hpp +@@ -31,7 +31,7 @@ + #include <iostream> + #include <gatb/system/api/types.hpp> + #include <gatb/tools/misc/api/Abundance.hpp> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + /********************************************************************************/ + namespace gatb { +diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp +index 3cb84f8..cd5d382 100644 +--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp ++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/Abundance.hpp +@@ -31,7 +31,7 @@ + /********************************************************************************/ + + #include <sys/types.h> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + /********************************************************************************/ + namespace gatb { +diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp +index b8f6c79..a040832 100644 +--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp ++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp +@@ -28,7 +28,7 @@ + + #include <gatb/system/api/ISmartPointer.hpp> + #include <gatb/tools/storage/impl/Storage.hpp> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + /********************************************************************************/ + namespace gatb { +diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp +index 2645abd..fad48c0 100644 +--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp ++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp +@@ -40,7 +40,7 @@ + #include <string> + #include <vector> + #include <stdarg.h> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + /********************************************************************************/ + namespace gatb { +diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp +index a92b729..66d552f 100644 +--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp ++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5Patch.hpp +@@ -40,7 +40,7 @@ + #include <string> + #include <vector> + #include <stdarg.h> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + + /********************************************************************************/ + namespace gatb { +diff --git a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp +index 29e0949..0565cc4 100644 +--- a/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp ++++ b/thirdparty/gatb-core/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp +@@ -33,7 +33,7 @@ + #include <gatb/tools/storage/impl/CollectionHDF5.hpp> + #include <gatb/tools/storage/impl/CollectionHDF5Patch.hpp> + #include <gatb/system/impl/System.hpp> +-#include <hdf5/hdf5.h> ++#include <hdf5.h> + #include <sstream> + + /********************************************************************************/ +diff --git a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt +index 6e0b5c4..34aef28 100644 +--- a/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt ++++ b/thirdparty/gatb-core/gatb-core/thirdparty/CMakeLists.txt +@@ -1,54 +1,3 @@ +-################################################################################ +-# HDF5 GENERATION +-################################################################################ +- +-#SET (HDF5_ENABLE_THREADSAFE ON) +-#SET (H5_HAVE_THREADSAFE 1) +- +-########## MOMENTARY DEACTIVATED => CRASH ON MACOS TO BE INVESTIGATED ########## +-SET (HDF5_BUILD_TOOLS ON CACHE BOOL "Build HDF5 Tools") +-#SET (CMAKE_EXE_LINKER_FLAGS "-lpthread -lz") +- +-SET (HDF5_EXTERNALLY_CONFIGURED ON) +- +-#SET (HDF5_INSTALL_BIN_DIR ${PROJECT_BINARY_DIR}/bin/${CMAKE_BUILD_TYPE}) +-#SET (HDF5_INSTALL_LIB_DIR ${PROJECT_BINARY_DIR}/lib/${CMAKE_BUILD_TYPE}) +-SET (HDF5_INSTALL_BIN_DIR bin) +-SET (HDF5_INSTALL_LIB_DIR lib) +- +-SET (HDF5_INSTALL_INCLUDE_DIR ${PROJECT_BINARY_DIR}/include/${CMAKE_BUILD_TYPE}/hdf5) +-SET (HDF5_INSTALL_DATA_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE}) +-SET (HDF5_INSTALL_CMAKE_DIR ${PROJECT_BINARY_DIR}/share/${CMAKE_BUILD_TYPE}) +- +-IF (NOT DEFINED GATB_CORE_INSTALL_EXCLUDE) +- SET (HDF5_EXPORTED_TARGETS "gatb-hdf5") +-ENDIF() +- +-IF (NOT DEFINED GATB_CORE_EXCLUDE_HDF5_ZLIB) +- OPTION (HDF5_ENABLE_Z_LIB_SUPPORT "Enable Zlib Filters" ON) +-ENDIF() +- +-# We don't want warnings from HDF5 compilation +-set (COMPILE_DEFINITIONS "${COMPILE_DEFINITIONS} -w") +-add_definitions (${COMPILE_DEFINITIONS}) +- +-# add HDF5 generation +-ADD_SUBDIRECTORY (hdf5) +- +-# We add a custom target for copying header files. +-add_custom_target (hdf5_postbuild ALL) +- +-# We build the output directory +-add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E make_directory ${HDF5_INSTALL_INCLUDE_DIR}) +- +-# We define all the header files to be copied +-file (GLOB headerfiles ${PROJECT_SOURCE_DIR}/thirdparty/hdf5/src/*.h ${PROJECT_BINARY_DIR}/thirdparty/hdf5/H5pubconf.h) +- +-# We copy each header file +-foreach (header ${headerfiles}) +- add_custom_command (TARGET hdf5_postbuild POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy_if_different ${header} ${HDF5_INSTALL_INCLUDE_DIR} ) +-endforeach() +- + # include other smaller libraries (json, Boophf) + + add_custom_target (thirdparty_copy ALL) diff --git a/nixpkgs/pkgs/applications/science/biology/niftyreg/default.nix b/nixpkgs/pkgs/applications/science/biology/niftyreg/default.nix index 6379f2c32826..48bd1b21ecd6 100644 --- a/nixpkgs/pkgs/applications/science/biology/niftyreg/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/niftyreg/default.nix @@ -9,6 +9,8 @@ stdenv.mkDerivation rec { sha256 = "07v9v9s41lvw72wpb1jgh2nzanyc994779bd35p76vg8mzifmprl"; }; + NIX_CFLAGS_COMPILE = [ "-Wno-error=narrowing" ]; + nativeBuildInputs = [ cmake ]; buildInputs = [ zlib ]; enableParallelBuilding = true; diff --git a/nixpkgs/pkgs/applications/science/biology/niftyseg/default.nix b/nixpkgs/pkgs/applications/science/biology/niftyseg/default.nix index 689d3e42c979..f70054e97716 100644 --- a/nixpkgs/pkgs/applications/science/biology/niftyseg/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/niftyseg/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { homepage = http://cmictig.cs.ucl.ac.uk/research/software/software-nifty/niftyseg; description = "Software for medical image segmentation, bias field correction, and cortical thickness calculation"; maintainers = with maintainers; [ bcdarwin ]; - platforms = platforms.linux; + platforms = platforms.unix; license = licenses.bsd3; }; diff --git a/nixpkgs/pkgs/applications/science/biology/paml/default.nix b/nixpkgs/pkgs/applications/science/biology/paml/default.nix index 161188f7ef16..731e31c588fa 100644 --- a/nixpkgs/pkgs/applications/science/biology/paml/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/paml/default.nix @@ -1,11 +1,11 @@ {stdenv, fetchurl}: stdenv.mkDerivation rec { - version = "4.9i"; + version = "4.9j"; pname = "paml"; src = fetchurl { url = "http://abacus.gene.ucl.ac.uk/software/paml${version}.tgz"; - sha256 = "1k5lcyls6c33ppp5fxl8ply2fy7i2k0gcqaifsl7gnc81d8ay4dw"; + sha256 = "0qflf3i27x6jwks3c6q560m1q8r043ja96syah145113iz5wdalp"; }; preBuild = '' diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix index 2a57febe8f5d..a67653c84373 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 = "2.21.3"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "107zlvp74ahpn652nfkipp80bbzf3fp812pi1ma42njk4wchah10"; + sha256 = "0s1gn2bkya41866kd8zj0g8xjbivs763jqmlzdpjz4c25h6xkhns"; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/nixpkgs/pkgs/applications/science/biology/spades/default.nix b/nixpkgs/pkgs/applications/science/biology/spades/default.nix new file mode 100644 index 000000000000..a195f79010a7 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/spades/default.nix @@ -0,0 +1,27 @@ +{ stdenv, fetchurl, zlib, bzip2, cmake }: + +stdenv.mkDerivation rec { + pname = "SPAdes"; + version = "3.13.1"; + + src = fetchurl { + url = "http://cab.spbu.ru/files/release${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/star/default.nix b/nixpkgs/pkgs/applications/science/biology/star/default.nix index f32dca86bdf5..6f4211d0c0d9 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 = "2.7.1a"; + version = "2.7.3a"; src = fetchFromGitHub { repo = "STAR"; owner = "alexdobin"; rev = version; - sha256 = "0n6g4s4hgw7qygs1z97j7a2dgz8gfaa4cv5pjvvvmarvk0x07hyg"; + sha256 = "1hgiqw5qhs0pc1xazzihcfd92na02xyq2kb469z04y1v51kpvvjq"; }; sourceRoot = "source/source"; diff --git a/nixpkgs/pkgs/applications/science/biology/strelka/default.nix b/nixpkgs/pkgs/applications/science/biology/strelka/default.nix index 84c90d895566..184dcb48a0de 100644 --- a/nixpkgs/pkgs/applications/science/biology/strelka/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/strelka/default.nix @@ -14,6 +14,11 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; buildInputs = [ zlib python2 ]; + NIX_CFLAGS_COMPILE = [ + "-Wno-error=maybe-uninitialized" + "-Wno-error=pessimizing-move" + ]; + preConfigure = '' sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py patchShebangs . diff --git a/nixpkgs/pkgs/applications/science/biology/sumatools/default.nix b/nixpkgs/pkgs/applications/science/biology/sumatools/default.nix index f9042f300113..5230fcd2eb62 100644 --- a/nixpkgs/pkgs/applications/science/biology/sumatools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/sumatools/default.nix @@ -22,7 +22,7 @@ in rec { rev = "sumalib_v${version}"; sha256 = "0hwkrxzfz7m5wdjvmrhkjg8kis378iaqr5n4nhdhkwwhn8x1jn5a"; }; - makeFlags = "PREFIX=$(out)"; + makeFlags = [ "PREFIX=$(out)" ]; inherit meta; }; diff --git a/nixpkgs/pkgs/applications/science/biology/svaba/default.nix b/nixpkgs/pkgs/applications/science/biology/svaba/default.nix new file mode 100644 index 000000000000..ae8dc95d6fea --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/svaba/default.nix @@ -0,0 +1,42 @@ +{ stdenv, zlib, bzip2, lzma, fetchFromGitHub } : + +stdenv.mkDerivation rec { + version = "1.1.0"; + pname = "svaba"; + + src = fetchFromGitHub { + owner = "walaj"; + repo = pname; + rev = version; + sha256 = "1vv5mc9z5d22kgdy7mm27ya5aahnqgkcrskdr2405058ikk9g8kp"; + fetchSubmodules = true; + }; + + buildInputs = [ zlib bzip2 lzma ]; + + installPhase = '' + runHook preInstall + install -Dm555 src/svaba/svaba $out/bin/svaba + runHook postInstall + ''; + + meta = with stdenv.lib; { + description = "Structural variant and INDEL caller for DNA sequencing data, using genome-wide local assembly"; + license = licenses.gpl3; + homepage = "https://github.com/walaj/svaba"; + maintainers = with maintainers; [ scalavision ]; + platforms = platforms.linux; + longDescription = '' + SvABA is a method for detecting structural variants in sequencing data + using genome-wide local assembly. Under the hood, SvABA uses a custom + implementation of SGA (String Graph Assembler) by Jared Simpson, + and BWA-MEM by Heng Li. Contigs are assembled for every 25kb window + (with some small overlap) for every region in the genome. + The default is to use only clipped, discordant, unmapped and indel reads, + although this can be customized to any set of reads at the command line using VariantBam rules. + These contigs are then immediately aligned to the reference with BWA-MEM and parsed to identify variants. + Sequencing reads are then realigned to the contigs with BWA-MEM, and variants are scored by their read support. + ''; + + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix b/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix new file mode 100644 index 000000000000..9ff81944f6a7 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/tebreak/default.nix @@ -0,0 +1,42 @@ +{ stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa +, samtools, findutils }: + +python3Packages.buildPythonApplication rec { + pname = "tebreak"; + version = "1.0"; + + src = fetchFromGitHub { + owner = "adamewing"; + repo = "tebreak"; + rev = version; + sha256 = "194av17wz66n4zxyi56mbkik31j2wmkly5i9qmxgaxymhavzi3kq"; + }; + + nativeBuildInputs = [ findutils python3Packages.cython ]; + propagatedBuildInputs = with python3Packages; [ + pysam + scipy + bx-python + scikit-bio + ]; + + preConfigure = '' + # patch the paths to all required software + for f in $(find . -type f) ; do + sed -i "s|'bwa'|'${bwa}/bin/bwa'|" $f + sed -i "s|'minia'|'${minia}/bin/minia'|" $f + sed -i "s|'exonerate'|'${exonerate}/bin/exonerate'|" $f + sed -i "s|'samtools'|'${samtools}/bin/samtools'|" $f + sed -i "s|'lastal'|'${last}/bin/lastal'|" $f + sed -i "s|'lastdb'|'${last}/bin/lastdb'|" $f + done + ''; + + meta = with stdenv.lib; { + description = "Find and characterise transposable element insertions"; + homepage = "https://github.com/adamewing/tebreak"; + license = licenses.mit; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.x86_64; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/truvari/default.nix b/nixpkgs/pkgs/applications/science/biology/truvari/default.nix new file mode 100644 index 000000000000..bee43da6719d --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/truvari/default.nix @@ -0,0 +1,43 @@ +{ lib +, fetchFromGitHub +, python3Packages +}: + +python3Packages.buildPythonApplication rec { + pname = "truvari"; + version = "1.3.2"; + + src = fetchFromGitHub { + owner = "spiralgenetics"; + repo = "truvari"; + rev = "v${version}"; + sha256 = "0wmjz8nzibvj0ixky1m0qi7iyd204prk7glbvig1cvaab33k19f1"; + }; + + propagatedBuildInputs = with python3Packages; [ + pyvcf + python-Levenshtein + progressbar2 + pysam + pyfaidx + intervaltree + ]; + + prePatch = '' + substituteInPlace ./setup.py \ + --replace '"progressbar2==3.41.0",' "" \ + --replace '"pysam==0.15.2",' "" + ''; + + meta = with lib; { + description = "Structural variant comparison tool for VCFs"; + license = licenses.mit; + maintainers = with maintainers; [ scalavision ]; + longDescription = '' + Truvari is a benchmarking tool for comparison sets of SVs. + It can calculate the recall, precision, and f-measure of a + vcf from a given structural variant caller. The tool + is created by Spiral Genetics. + ''; + }; +} |