diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology')
56 files changed, 1758 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix b/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix new file mode 100644 index 000000000000..dbcfead6b1ea --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/EZminc/default.nix @@ -0,0 +1,30 @@ +{ stdenv, fetchFromGitHub, cmake, libminc, bicpl, itk, fftwFloat, gsl }: + +stdenv.mkDerivation rec { pname = "EZminc"; + name = "${pname}-2017-08-29"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "4e017236cb6e7f6e07507446b18b759c584b6fc3"; + sha256 = "1pg06x42pgsg7zy7dz9wf6ajakkm2n8by64lg9z64qi8qqy82b8v"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ itk libminc bicpl fftwFloat gsl ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" + "-DEZMINC_BUILD_TOOLS=TRUE" + "-DEZMINC_BUILD_MRFSEG=TRUE" + "-DEZMINC_BUILD_DD=TRUE" ]; + + enableParallelBuilding = true; + + meta = with stdenv.lib; { + homepage = "https://github.com/BIC-MNI/${pname}"; + description = "Collection of Perl and shell scripts for processing MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/N3/default.nix b/nixpkgs/pkgs/applications/science/biology/N3/default.nix new file mode 100644 index 000000000000..d2dbcf185330 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/N3/default.nix @@ -0,0 +1,35 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, + perlPackages, + libminc, EBTKS }: + +stdenv.mkDerivation rec { + pname = "N3"; + name = "${pname}-2017-09-18"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "2fdd939f0f2b24a4039bc6a8ade4a190a1d8e75d"; + sha256 = "13z21c4r09hna3q1csvcn4i7ws5ixbdaja6ch421xv6nydjh2w5g"; + }; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ libminc EBTKS ]; + propagatedBuildInputs = with perlPackages; [ perl MNI-Perllib GetoptTabular ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ]; + + postFixup = '' + for p in $out/bin/*; do + wrapProgram $p --prefix PERL5LIB : $PERL5LIB + done + ''; + + meta = with stdenv.lib; { + homepage = "https://github.com/BIC-MNI/${pname}"; + description = "MRI non-uniformity correction for MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/ants/default.nix b/nixpkgs/pkgs/applications/science/biology/ants/default.nix new file mode 100644 index 000000000000..f54bd9af0288 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/ants/default.nix @@ -0,0 +1,37 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, itk, vtk }: + +stdenv.mkDerivation rec { + _name = "ANTs"; + _version = "2.2.0"; + name = "${_name}-${_version}"; + + src = fetchFromGitHub { + owner = "ANTsX"; + repo = "ANTs"; + rev = "37ad4e20be3a5ecd26c2e4e41b49e778a0246c3d"; + sha256 = "1hrdwv3m9xh3yf7l0rm2ggxc2xzckfb8srs88g485ibfszx7i03q"; + }; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ itk vtk ]; + + cmakeFlags = [ "-DANTS_SUPERBUILD=FALSE" "-DUSE_VTK=TRUE" + # as cmake otherwise tries to download test data: + "-DBUILD_TESTING=FALSE" ]; + + enableParallelBuilding = true; + + postInstall = '' + for file in $out/bin/*; do + wrapProgram $file --set ANTSPATH "$out/bin" + done + ''; + + meta = with stdenv.lib; { + homepage = https://github.com/ANTxS/ANTs; + description = "Advanced normalization toolkit for medical image registration and other processing"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.bsd3; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix b/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix new file mode 100644 index 000000000000..539d7c224463 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/bcftools/default.nix @@ -0,0 +1,38 @@ +{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, python, bash }: + +stdenv.mkDerivation rec { + name = "${pname}-${version}"; + pname = "bcftools"; + version = "1.9"; + + src = fetchurl { + url = "https://github.com/samtools/bcftools/releases/download/${version}/${name}.tar.bz2"; + sha256 = "1j3h638i8kgihzyrlnpj82xg1b23sijibys9hvwari3fy7kd0dkg"; + }; + + buildInputs = [ htslib zlib bzip2 lzma curl perl python ]; + + makeFlags = [ + "HSTDIR=${htslib}" + "prefix=$(out)" + "CC=cc" + ]; + + preCheck = '' + patchShebangs misc/ + patchShebangs test/ + sed -ie 's|/bin/bash|${bash}/bin/bash|' test/test.pl + ''; + + enableParallelBuilding = true; + + doCheck = true; + + meta = with stdenv.lib; { + description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants"; + license = licenses.mit; + homepage = http://www.htslib.org/; + platforms = platforms.unix; + maintainers = [ maintainers.mimadrid ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix new file mode 100644 index 000000000000..406f42e9ad7b --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix @@ -0,0 +1,26 @@ +{stdenv, fetchFromGitHub, zlib, python}: + +stdenv.mkDerivation rec { + name = "bedtools-${version}"; + version = "2.27.1"; + + src = fetchFromGitHub { + owner = "arq5x"; + repo = "bedtools2"; + rev = "v${version}"; + sha256 = "1pk68y052rm2m24yfmy82ms8p6kd6xcqxxgi7n0a1sbh89wllm6s"; + }; + + buildInputs = [ zlib python ]; + cc = if stdenv.cc.isClang then "clang++" else "g++"; + buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} -j $NIX_BUILD_CORES"; + installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} install"; + + 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/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/bowtie2/default.nix b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix new file mode 100644 index 000000000000..e97b5d1a3f4f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix @@ -0,0 +1,27 @@ +{ stdenv, fetchFromGitHub, zlib, tbb, python, perl }: + +stdenv.mkDerivation rec { + pname = "bowtie2"; + version = "2.3.4.3"; + name = "${pname}-${version}"; + + src = fetchFromGitHub { + owner = "BenLangmead"; + repo = pname; + rev = "v${version}"; + sha256 = "1zl3cf327y2p7p03cavymbh7b00djc7lncfaqih33n96iy9q8ibp"; + }; + + buildInputs = [ zlib tbb python perl ]; + + installFlags = [ "prefix=$(out)" ]; + + meta = with stdenv.lib; { + description = "An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences"; + license = licenses.gpl3; + homepage = http://bowtie-bio.sf.net/bowtie2; + maintainers = with maintainers; [ rybern ]; + platforms = platforms.all; + broken = stdenv.isAarch64; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/bwa/default.nix b/nixpkgs/pkgs/applications/science/biology/bwa/default.nix new file mode 100644 index 000000000000..d1dbacf053fb --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/bwa/default.nix @@ -0,0 +1,25 @@ +{ stdenv, fetchurl, zlib }: + +stdenv.mkDerivation rec { + name = "bwa-${version}"; + version = "0.7.17"; + + src = fetchurl { + url = "mirror://sourceforge/bio-bwa/${name}.tar.bz2"; + sha256 = "1zfhv2zg9v1icdlq4p9ssc8k01mca5d1bd87w71py2swfi74s6yy"; + }; + + buildInputs = [ zlib ]; + + installPhase = '' + install -vD bwa $out/bin/bwa + ''; + + meta = with stdenv.lib; { + description = "A software package for mapping low-divergent sequences against a large reference genome, such as the human genome"; + license = licenses.gpl3; + homepage = http://bio-bwa.sourceforge.net/; + maintainers = with maintainers; [ luispedro ]; + platforms = [ "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/cmtk/default.nix b/nixpkgs/pkgs/applications/science/biology/cmtk/default.nix new file mode 100644 index 000000000000..ed661db23e0a --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/cmtk/default.nix @@ -0,0 +1,24 @@ +{stdenv, fetchurl, cmake}: + +stdenv.mkDerivation rec { + name = "cmtk-3.3.1"; + + src = fetchurl { + name = "cmtk-source.tar.gz"; + url = "https://www.nitrc.org/frs/download.php/8198/CMTK-3.3.1-Source.tar.gz//?i_agree=1&download_now=1"; + sha256 = "1nmsga9m7vcc4y4a6zl53ra3mwlgjwdgsq1j291awkn7zr1az6qs"; + }; + + buildInputs = [cmake]; + + meta = with stdenv.lib; { + description = "Computational Morphometry Toolkit "; + longDescription = ''A software toolkit for computational morphometry of + biomedical images, CMTK comprises a set of command line tools and a + back-end general-purpose library for processing and I/O''; + maintainers = with maintainers; [ tbenst ]; + platforms = platforms.all; + license = licenses.gpl3; + homepage = https://www.nitrc.org/projects/cmtk/; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix b/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix new file mode 100644 index 000000000000..23182fcadc6b --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/conglomerate/default.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchFromGitHub, cmake, coreutils, perlPackages, bicpl, libminc, zlib, minc_tools, + makeWrapper }: + +stdenv.mkDerivation rec { + pname = "conglomerate"; + name = "${pname}-2017-09-10"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "7343238bc6215942c7ecc885a224f24433a291b0"; + sha256 = "1mlqgmy3jc13bv7d01rjwldxq0p4ayqic85xcl222hhifi3w2prr"; + }; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ libminc zlib bicpl ]; + propagatedBuildInputs = [ coreutils minc_tools ] ++ (with perlPackages; [ perl GetoptTabular MNI-Perllib ]); + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBICPL_DIR=${bicpl}/lib/" ]; + + postFixup = '' + for p in $out/bin/*; do + wrapProgram $p --prefix PERL5LIB : $PERL5LIB --set PATH "${stdenv.lib.makeBinPath [ coreutils minc_tools ]}"; + done + ''; + + meta = with stdenv.lib; { + homepage = https://github.com/BIC-MNI/conglomerate; + description = "More command-line utilities for working with MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix new file mode 100644 index 000000000000..781ceb3df59e --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix @@ -0,0 +1,33 @@ +{ stdenv +, fetchFromGitHub +, cmake +, libyamlcpp +}: + +stdenv.mkDerivation rec { + version = "1.0.20170130"; + name = "dcm2niix-${version}"; + + src = fetchFromGitHub { + owner = "rordenlab"; + repo = "dcm2niix"; + rev = "v${version}"; + sha256 = "1f2nzd8flp1rfn725bi64z7aw3ccxyyygzarxijw6pvgl476i532"; + }; + + enableParallelBuilding = true; + nativeBuildInputs = [ cmake ]; + buildInputs = [ libyamlcpp ]; + + meta = with stdenv.lib; { + description = "dcm2niix DICOM to NIfTI converter"; + longDescription = '' + dcm2niix is a designed to convert neuroimaging data from the + DICOM format to the NIfTI format. + ''; + homepage = https://www.nitrc.org/projects/dcm2nii; + license = licenses.bsd3; + maintainers = [ maintainers.ashgillman ]; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/diamond/default.nix b/nixpkgs/pkgs/applications/science/biology/diamond/default.nix new file mode 100644 index 000000000000..854e91b2fcbb --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/diamond/default.nix @@ -0,0 +1,41 @@ +{ stdenv, fetchurl, cmake, zlib }: + +stdenv.mkDerivation rec { + name = "diamond-0.8.36"; + + src = fetchurl { + url = "https://github.com/bbuchfink/diamond/archive/v0.8.36.tar.gz"; + sha256 = "092smzzjcg51n3x4h84k52ijpz9m40ri838j9k2i463ribc3c8rh"; + }; + + patches = [ + ./diamond-0.8.36-no-warning.patch + ]; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ zlib ]; + + meta = with stdenv.lib; { + description = "Accelerated BLAST compatible local sequence aligner"; + longDescription = '' + A sequence aligner for protein and translated DNA + searches and functions as a drop-in replacement for the NCBI BLAST + software tools. It is suitable for protein-protein search as well as + DNA-protein search on short reads and longer sequences including contigs + and assemblies, providing a speedup of BLAST ranging up to x20,000. + + DIAMOND is developed by Benjamin Buchfink. Feel free to contact him for support (Email Twitter). + + If you use DIAMOND in published research, please cite + B. Buchfink, Xie C., D. Huson, + "Fast and sensitive protein alignment using DIAMOND", + Nature Methods 12, 59-60 (2015). + ''; + homepage = https://github.com/bbuchfink/diamond; + license = { + fullName = "University of Tuebingen, Benjamin Buchfink"; + url = https://raw.githubusercontent.com/bbuchfink/diamond/master/src/COPYING; + }; + maintainers = [ maintainers.metabar ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch b/nixpkgs/pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch new file mode 100644 index 000000000000..a16d475c5564 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/diamond/diamond-0.8.36-no-warning.patch @@ -0,0 +1,20 @@ +diff -u -r diamond-0.8.36/src/dp/scalar_traceback.h diamond-0.8.36-patched/src/dp/scalar_traceback.h +--- diamond-0.8.36/src/dp/scalar_traceback.h 2017-02-06 16:32:05.000000000 +0100 ++++ diamond-0.8.36-patched/src/dp/scalar_traceback.h 2017-02-23 15:13:24.000000000 +0100 +@@ -19,6 +19,7 @@ + #ifndef SCALAR_TRACEBACK_H_ + #define SCALAR_TRACEBACK_H_ + ++#include <cmath> + #include <exception> + #include "../basic/score_matrix.h" + +@@ -31,7 +32,7 @@ + template<> + inline bool almost_equal<float>(float x, float y) + { +- return abs(x - y) < 0.001f; ++ return std::abs(x - y) < 0.001f; + } + + template<typename _score> diff --git a/nixpkgs/pkgs/applications/science/biology/ecopcr/default.nix b/nixpkgs/pkgs/applications/science/biology/ecopcr/default.nix new file mode 100644 index 000000000000..9e1b16ff9449 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/ecopcr/default.nix @@ -0,0 +1,37 @@ +{ stdenv, fetchurl, gcc, zlib, python27 }: + +stdenv.mkDerivation rec { + name = "ecopcr-0.8.0"; + + src = fetchurl { + url = "https://git.metabarcoding.org/obitools/ecopcr/uploads/6f37991b325c8c171df7e79e6ae8d080/${name}.tar.gz"; + sha256 = "10c58hj25z78jh0g3zcbx4890yd2qrvaaanyx8mn9p49mmyf5pk6"; + }; + + sourceRoot = "ecoPCR/src"; + + buildInputs = [ gcc python27 zlib ]; + + installPhase = '' + mkdir -p $out/bin + cp -v ecoPCR $out/bin + cp -v ecogrep $out/bin + cp -v ecofind $out/bin + cp -v ../tools/ecoPCRFormat.py $out/bin/ecoPCRFormat + chmod a+x $out/bin/ecoPCRFormat + ''; + + meta = with stdenv.lib; { + description = "Electronic PCR software tool"; + longDescription = '' + ecoPCR is an electronic PCR software developed by the LECA. It + helps you estimate Barcode primers quality. In conjunction with + OBITools, you can postprocess ecoPCR output to compute barcode + coverage and barcode specificity. New barcode primers can be + developed using the ecoPrimers software. + ''; + homepage = https://git.metabarcoding.org/obitools/ecopcr/wikis/home; + license = licenses.cecill20; + maintainers = [ maintainers.metabar ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/emboss/default.nix b/nixpkgs/pkgs/applications/science/biology/emboss/default.nix new file mode 100644 index 000000000000..2110a9bcfaba --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/emboss/default.nix @@ -0,0 +1,28 @@ +{stdenv, fetchurl, readline, perl, libharu, libX11, libpng, libXt, zlib}: + +stdenv.mkDerivation { + name = "emboss-6.6.0"; + src = fetchurl { + url = "ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz"; + sha256 = "7184a763d39ad96bb598bfd531628a34aa53e474db9e7cac4416c2a40ab10c6e"; + }; + + buildInputs = [ readline perl libharu libpng libX11 libXt zlib ]; + + configureFlags = [ "--with-hpdf=${libharu}" "--with-pngdriver=${zlib}" ]; + + postConfigure = '' + sed -i 's@$(bindir)/embossupdate@true@' Makefile + ''; + + meta = { + description = "The European Molecular Biology Open Software Suite"; + longDescription = ''EMBOSS is a free Open Source software analysis package + specially developed for the needs of the molecular biology (e.g. EMBnet) + user community, including libraries. The software automatically copes with + data in a variety of formats and even allows transparent retrieval of + sequence data from the web.''; + license = "GPL2"; + homepage = http://emboss.sourceforge.net/; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix b/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix new file mode 100644 index 000000000000..1a15dcf6197d --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/freebayes/default.nix @@ -0,0 +1,29 @@ +{ stdenv, fetchFromGitHub, zlib, bzip2, lzma }: + +stdenv.mkDerivation rec { + name = "freebayes-${version}"; + version = "2017-08-23"; + + src = fetchFromGitHub { + name = "freebayes-${version}-src"; + owner = "ekg"; + repo = "freebayes"; + rev = "8d2b3a060da473e1f4f89be04edfce5cba63f1d3"; + sha256 = "0yyrgk2639lz1yvg4jf0ccahnkic31dy77q05pb3i28rjf37v45z"; + fetchSubmodules = true; + }; + + buildInputs = [ zlib bzip2 lzma ]; + + installPhase = '' + install -vD bin/freebayes bin/bamleftalign scripts/* -t $out/bin + ''; + + meta = with stdenv.lib; { + description = "Bayesian haplotype-based polymorphism discovery and genotyping"; + license = licenses.mit; + homepage = https://github.com/ekg/freebayes; + maintainers = with maintainers; [ jdagilliland ]; + platforms = [ "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix b/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix new file mode 100644 index 000000000000..9ccf54a81133 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix @@ -0,0 +1,49 @@ +{stdenv, fetchurl, unzip, which, python}: + +stdenv.mkDerivation rec { + name = "hisat2-${version}"; + version = "2.1.0"; + + src = fetchurl { + url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-${version}-source.zip"; + sha256 = "10g73sdf6vqqfhhd92hliw7bbpkb8v4pp5012r5l21zws7p7d8l9"; + }; + + buildInputs = [ unzip which python ]; + + installPhase = '' + mkdir -p $out/bin + cp hisat2 \ + hisat2-inspect-l \ + hisat2-build-s \ + hisat2-align-l \ + hisat2-inspect \ + hisat2-align-s \ + hisat2-inspect-s \ + hisat2-build-l \ + hisat2-build \ + extract_exons.py \ + extract_splice_sites.py \ + hisat2_extract_exons.py \ + hisat2_extract_snps_haplotypes_UCSC.py \ + hisat2_extract_snps_haplotypes_VCF.py \ + hisat2_extract_splice_sites.py \ + hisat2_simulate_reads.py \ + hisatgenotype_build_genome.py \ + hisatgenotype_extract_reads.py \ + hisatgenotype_extract_vars.py \ + hisatgenotype_hla_cyp.py \ + hisatgenotype_locus.py \ + hisatgenotype.py \ + $out/bin + ''; + + meta = with stdenv.lib; { + description = "Graph based aligner"; + license = licenses.gpl3; + homepage = https://ccb.jhu.edu/software/hisat2/index.shtml; + maintainers = with maintainers; [ jbedo ]; + platforms = [ "x86_64-linux" "i686-linux" ]; + }; + +} diff --git a/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix b/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix new file mode 100644 index 000000000000..e43d48db55f3 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/hmmer/default.nix @@ -0,0 +1,25 @@ +{ stdenv, fetchurl }: + +stdenv.mkDerivation rec { + version = "3.2.1"; + name = "hmmer-${version}"; + + src = fetchurl { + url = "http://eddylab.org/software/hmmer/${name}.tar.gz"; + sha256 = "171bivy6xhgjsz5nv53n81pc3frnwz29ylblawk2bv46szwjjqd5"; + }; + + meta = with stdenv.lib; { + description = "Biosequence analysis using profile hidden Markov models"; + longDescription = '' + HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). + HMMER is often used together with a profile database, such as Pfam or many of the databases that participate in Interpro. But HMMER can also work with query sequences, not just profiles, just like BLAST. For example, you can search a protein query sequence against a database with phmmer, or do an iterative search with jackhmmer. + HMMER is designed to detect remote homologs as sensitively as possible, relying on the strength of its underlying probability models. In the past, this strength came at significant computational expense, but as of the new HMMER3 project, HMMER is now essentially as fast as BLAST. + HMMER can be downloaded and installed as a command line tool on your own hardware, and now it is also more widely accessible to the scientific community via new search servers at the European Bioinformatics Institute. + ''; + homepage = http://hmmer.org/; + license = licenses.gpl3; + maintainers = [ maintainers.iimog ]; + platforms = [ "x86_64-linux" "i686-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/igv/default.nix b/nixpkgs/pkgs/applications/science/biology/igv/default.nix new file mode 100644 index 000000000000..95dc2b612e22 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/igv/default.nix @@ -0,0 +1,33 @@ +{ stdenv, fetchurl, unzip, jre }: + +stdenv.mkDerivation rec { + name = "igv-${version}"; + version = "2.4.19"; + + src = fetchurl { + url = "https://data.broadinstitute.org/igv/projects/downloads/2.4/IGV_${version}.zip"; + sha256 = "048dgrhxcb854d24kyjkqz12bw04bsv49i5jawb75yzkswwfkb0z"; + }; + + buildInputs = [ unzip jre ]; + + installPhase = '' + mkdir -pv $out/{share,bin} + cp -Rv * $out/share/ + + sed -i "s#prefix=.*#prefix=$out/share#g" $out/share/igv.sh + sed -i 's#java#${jre}/bin/java#g' $out/share/igv.sh + + ln -s $out/share/igv.sh $out/bin/igv + + chmod +x $out/bin/igv + ''; + + meta = with stdenv.lib; { + homepage = https://www.broadinstitute.org/igv/; + description = "A visualization tool for interactive exploration of genomic datasets"; + license = licenses.lgpl21; + platforms = platforms.unix; + maintainers = [ maintainers.mimadrid ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix b/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix new file mode 100644 index 000000000000..9e63b92b24ed --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix @@ -0,0 +1,37 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, + perlPackages, + libminc, EBTKS }: + +stdenv.mkDerivation rec { + pname = "inormalize"; + name = "${pname}-2014-10-21"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "79cea9cdfe7b99abfd40afda89ab2253b596ad2f"; + sha256 = "1ahqv5q0ljvji99a5q8azjkdf6bgp6nr8lwivkqwqs3jm0k5clq7"; + }; + + patches = [ ./lgmask-interp.patch ./nu_correct_norm-interp.patch ]; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ libminc EBTKS ]; + propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DEBTKS_DIR=${EBTKS}/lib/" ]; + + postFixup = '' + for p in $out/bin/*; do + wrapProgram $p --prefix PERL5LIB : $PERL5LIB + done + ''; + + meta = with stdenv.lib; { + homepage = "https://github.com/BIC-MNI/${pname}"; + description = "Program to normalize intensity of MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/inormalize/lgmask-interp.patch b/nixpkgs/pkgs/applications/science/biology/inormalize/lgmask-interp.patch new file mode 100644 index 000000000000..953bce9a1848 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/inormalize/lgmask-interp.patch @@ -0,0 +1,10 @@ +diff --git a/lgmask.in b/lgmask.in +index 17dbe4d..2195d91 100644 +--- a/lgmask.in ++++ b/lgmask.in +@@ -1,4 +1,4 @@ +-#! @PERL@ ++#! /usr/bin/env perl + + #--------------------------------------------------------------------------- + #@COPYRIGHT : diff --git a/nixpkgs/pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch b/nixpkgs/pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch new file mode 100644 index 000000000000..75dc46a799ce --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/inormalize/nu_correct_norm-interp.patch @@ -0,0 +1,10 @@ +diff --git a/nu_correct_norm.in b/nu_correct_norm.in +index 1dc84ac..1bc6235 100644 +--- a/nu_correct_norm.in ++++ b/nu_correct_norm.in +@@ -1,4 +1,4 @@ +-#! @PERL@ ++#! /usr/bin/perl + + #--------------------------------------------------------------------------- + #@COPYRIGHT : diff --git a/nixpkgs/pkgs/applications/science/biology/iv/default.nix b/nixpkgs/pkgs/applications/science/biology/iv/default.nix new file mode 100644 index 000000000000..f204d9bbca96 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/iv/default.nix @@ -0,0 +1,31 @@ +{ stdenv, fetchurl, neuron-version +, libX11, libXext, patchelf +}: + +stdenv.mkDerivation rec + { name = "iv-19"; + src = fetchurl + { url = "https://www.neuron.yale.edu/ftp/neuron/versions/v${neuron-version}/${name}.tar.gz"; + sha256 = "07a3g8zzay4h0bls7fh89dd0phn7s34c2g15pij6dsnwpmjg06yx"; + }; + nativeBuildInputs = [ patchelf ]; + buildInputs = [ libXext ]; + propagatedBuildInputs = [ libX11 ]; + hardeningDisable = [ "format" ]; + postInstall = '' + for dir in $out/*; do # */ + if [ -d $dir/lib ]; then + mv $dir/* $out # */ + rmdir $dir + break + fi + done + patchelf --add-needed ${libX11}/lib/libX11.so $out/lib/libIVhines.so + ''; + meta = with stdenv.lib; + { description = "InterViews graphical library for Neuron"; + license = licenses.bsd3; + homepage = http://www.neuron.yale.edu/neuron; + platforms = platforms.all; + }; + } diff --git a/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix b/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix new file mode 100644 index 000000000000..d80ffea9a780 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/kallisto/default.nix @@ -0,0 +1,25 @@ +{ stdenv, fetchFromGitHub, cmake, hdf5, zlib }: + +stdenv.mkDerivation rec { + name = "kallisto-${version}"; + version = "0.43.1"; + + src = fetchFromGitHub { + repo = "kallisto"; + owner = "pachterlab"; + rev = "v${version}"; + sha256 = "04697pf7jvy7vw126s1rn09q4iab9223jvb1nb0jn7ilwkq7pgwz"; + }; + + nativeBuildInputs = [ cmake ]; + + buildInputs = [ hdf5 zlib ]; + + meta = with stdenv.lib; { + description = "kallisto is a program for quantifying abundances of transcripts from RNA-Seq data"; + homepage = https://pachterlab.github.io/kallisto; + license = licenses.bsd2; + platforms = platforms.linux; + maintainers = [ maintainers.arcadio ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix new file mode 100644 index 000000000000..033f78609e9a --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/minc-tools/default.nix @@ -0,0 +1,35 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, flex, bison, perlPackages, libminc, libjpeg, zlib }: + +stdenv.mkDerivation rec { + pname = "minc-tools"; + name = "${pname}-2017-09-11"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "5b7c40425cd4f67a018055cb85c0157ee50a3056"; + sha256 = "0zkcs05svp1gj5h0cdgc0k20c7lrk8m7wg3ks3xc5mkaiannj8g7"; + }; + + nativeBuildInputs = [ cmake flex bison makeWrapper ]; + buildInputs = [ libminc libjpeg zlib ]; + propagatedBuildInputs = with perlPackages; [ perl TextFormat ]; + + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ]; + + postFixup = '' + for prog in minccomplete minchistory mincpik; do + wrapProgram $out/bin/$prog --prefix PERL5LIB : $PERL5LIB + done + ''; + + enableParallelBuilding = true; + + meta = with stdenv.lib; { + homepage = https://github.com/BIC-MNI/minc-tools; + description = "Command-line utilities for working with MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/minc-widgets/default.nix b/nixpkgs/pkgs/applications/science/biology/minc-widgets/default.nix new file mode 100644 index 000000000000..497c39a52a4c --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/minc-widgets/default.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, + perlPackages, + libminc, octave, coreutils, minc_tools }: + +stdenv.mkDerivation rec { + pname = "minc-widgets"; + name = "${pname}-2016-04-20"; + + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "f08b643894c81a1a2e0fbfe595a17a42ba8906db"; + sha256 = "1b9g6lf37wpp211ikaji4rf74rl9xcmrlyqcw1zq3z12ji9y33bm"; + }; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ libminc ]; + propagatedBuildInputs = (with perlPackages; [ perl GetoptTabular MNI-Perllib ]) ++ [ octave coreutils minc_tools ]; + + postFixup = '' + for p in $out/bin/*; do + wrapProgram $p --prefix PERL5LIB : $PERL5LIB --set PATH "${stdenv.lib.makeBinPath [ coreutils minc_tools ]}"; + done + ''; + + meta = with stdenv.lib; { + homepage = "https://github.com/BIC-MNI/${pname}"; + description = "Collection of Perl and shell scripts for processing MINC files"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix b/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix new file mode 100644 index 000000000000..3f28b5e31ccd --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/minimap2/default.nix @@ -0,0 +1,31 @@ +{ stdenv, fetchFromGitHub, zlib }: + +stdenv.mkDerivation rec { + name = "${pname}-${version}"; + pname = "minimap2"; + version = "2.15"; + + src = fetchFromGitHub { + repo = pname; + owner = "lh3"; + rev = "v${version}"; + sha256 = "0dy3m2wjmi3whjnmkj3maa1aadz525h7736wm8vvdcwq71ijqb7v"; + }; + + buildInputs = [ zlib ]; + + installPhase = '' + mkdir -p $out/bin + cp minimap2 $out/bin + mkdir -p $out/share/man/man1 + cp minimap2.1 $out/share/man/man1 + ''; + + meta = with stdenv.lib; { + description = "A versatile pairwise aligner for genomic and spliced nucleotide sequences"; + homepage = https://lh3.github.io/minimap2; + license = licenses.mit; + platforms = platforms.all; + maintainers = [ maintainers.arcadio ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix b/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix new file mode 100644 index 000000000000..5901b696d642 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix @@ -0,0 +1,36 @@ +{ stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, libminc }: + +stdenv.mkDerivation rec { + pname = "mni_autoreg"; + name = "${pname}-2017-09-22"; + + src = fetchFromGitHub { + owner = "BIC-MNI"; + repo = pname; + rev = "ab99e29987dc029737785baebf24896ec37a2d76"; + sha256 = "0axl069nv57vmb2wvqq7s9v3bfxwspzmk37bxm4973ai1irgppjq"; + }; + + nativeBuildInputs = [ cmake makeWrapper ]; + buildInputs = [ libminc ]; + 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 + + postFixup = '' + for prog in autocrop mritoself mritotal xfmtool; do + echo $out/bin/$prog + wrapProgram $out/bin/$prog --prefix PERL5LIB : $PERL5LIB; + done + ''; + + meta = with stdenv.lib; { + homepage = https://github.com/BIC-MNI/mni_autoreg; + description = "Tools for automated registration using the MINC image format"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = platforms.unix; + license = licenses.free; + }; +} + diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix new file mode 100644 index 000000000000..3cd83a5cdd27 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix @@ -0,0 +1,45 @@ +{stdenv, fetchFromGitHub, nim, htslib, pcre}: + +let + hts-nim = fetchFromGitHub { + owner = "brentp"; + repo = "hts-nim"; + rev = "v0.2.5"; + sha256 = "1fma99rjqxgg9dihkd10hm1jjp5amsk5wsxnvq1lk4mcsjix5xqb"; + }; + + docopt = fetchFromGitHub { + owner = "docopt"; + repo = "docopt.nim"; + rev = "v0.6.5"; + sha256 = "0yx79m4jkdcazwlky55nwf39zj5kdhymrrdrjq29mahiwx83x5zr"; + }; + +in stdenv.mkDerivation rec { + name = "mosdepth-${version}"; + version = "0.2.3"; + + src = fetchFromGitHub { + owner = "brentp"; + repo = "mosdepth"; + rev = "v${version}"; + sha256 = "1b9frrwhcvay3alhn0d02jccc2qlbij1732hzq9nhwnr4kvsvxx7"; + }; + + buildInputs = [ nim ]; + + buildPhase = '' + HOME=$TMPDIR + nim -p:${hts-nim}/src -p:${docopt}/src c --nilseqs:on -d:release mosdepth.nim + ''; + installPhase = "install -Dt $out/bin mosdepth"; + fixupPhase = "patchelf --set-rpath ${stdenv.lib.makeLibraryPath [ stdenv.cc.cc htslib pcre ]} $out/bin/mosdepth"; + + meta = with stdenv.lib; { + description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing."; + license = licenses.mit; + homepage = https://github.com/brentp/mosdepth; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/mrbayes/builder.sh b/nixpkgs/pkgs/applications/science/biology/mrbayes/builder.sh new file mode 100644 index 000000000000..5b3a54946fc9 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/mrbayes/builder.sh @@ -0,0 +1,9 @@ +# builder for mrbayes - note: only builds on Unix + +source $stdenv/setup + +tar xvfz $src +cd mrbayes-* +make +mkdir -p $out/bin +cp -v mb $out/bin diff --git a/nixpkgs/pkgs/applications/science/biology/mrbayes/default.nix b/nixpkgs/pkgs/applications/science/biology/mrbayes/default.nix new file mode 100644 index 000000000000..1dd92af58eb1 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/mrbayes/default.nix @@ -0,0 +1,29 @@ +{stdenv, fetchurl, readline}: + +stdenv.mkDerivation rec { + # FIXME: replace Makefile so we can build MPI & MAC support + + name = "mrbayes-3.1.2"; + src = fetchurl { + url = "mirror://sourceforge/mrbayes/${name}.tar.gz"; + sha256 = "1x7j8ca5wjrqrxmcpvd375ydm3s2pbkzykv8xfhg1jc037g560n6"; + }; + builder = ./builder.sh; + buildInputs = [readline]; + + meta = { + description = "Bayesian Inference of Phylogeny"; + longDescription = '' + Bayesian inference of phylogeny is based upon a + quantity called the posterior probability distribution of trees, which is + the probability of a tree conditioned on the observations. The conditioning + is accomplished using Bayes's theorem. The posterior probability + distribution of trees is impossible to calculate analytically; instead, + MrBayes uses a simulation technique called Markov chain Monte Carlo (or + MCMC) to approximate the posterior probabilities of trees. + ''; + license = "GPL2"; + homepage = http://mrbayes.csit.fsu.edu/; + platforms = stdenv.lib.platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/muscle/default.nix b/nixpkgs/pkgs/applications/science/biology/muscle/default.nix new file mode 100644 index 000000000000..9cbabc7ab37e --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/muscle/default.nix @@ -0,0 +1,35 @@ +{ stdenv, fetchurl }: + +stdenv.mkDerivation rec { + _name = "muscle"; + name = "${_name}-${version}"; + version = "3.8.31"; + + src = fetchurl { + url = "https://www.drive5.com/muscle/downloads${version}/${_name}${version}_src.tar.gz"; + sha256 = "1b89z0x7h098g99g00nqadgjnb2r5wpi9s11b7ddffqkh9m9dia3"; + }; + + patches = [ + ./muscle-3.8.31-no-static.patch + ]; + + preBuild = '' + cd ./src/ + patchShebangs mk + ''; + + installPhase = '' + install -vD muscle $out/bin/muscle + ''; + + meta = with stdenv.lib; { + description = "A multiple sequence alignment method with reduced time and space complexity"; + license = licenses.publicDomain; + homepage = https://www.drive5.com/muscle/; + maintainers = [ maintainers.unode ]; + # NOTE: Supposed to be compatible with darwin/intel & PPC but currently fails. + # Anyone with access to these platforms is welcome to give it a try + platforms = stdenv.lib.platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/muscle/muscle-3.8.31-no-static.patch b/nixpkgs/pkgs/applications/science/biology/muscle/muscle-3.8.31-no-static.patch new file mode 100644 index 000000000000..7f4b2129518d --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/muscle/muscle-3.8.31-no-static.patch @@ -0,0 +1,21 @@ +--- a/src/mk 2010-05-02 01:15:42.000000000 +0200 ++++ b/src/mk 2018-01-27 17:07:23.539092748 +0100 +@@ -5,14 +5,14 @@ + rm -f *.o muscle.make.stdout.txt muscle.make.stderr.txt + for CPPName in $CPPNames + do +- echo $CPPName >> /dev/tty ++ echo $CPPName + g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt + done + + LINK_OPTS= +-if [ `uname -s` == Linux ] ; then +- LINK_OPTS=-static +-fi ++#if [ `uname -s` == Linux ] ; then ++# LINK_OPTS=-static ++#fi + g++ $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt + tail muscle.make.stderr.txt + diff --git a/nixpkgs/pkgs/applications/science/biology/ncbi-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/ncbi-tools/default.nix new file mode 100644 index 000000000000..1c24ef092542 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/ncbi-tools/default.nix @@ -0,0 +1,34 @@ +{stdenv, fetchurl, cpio}: + +# The NCBI package only builds on 32bits - on 64bits it breaks because +# of position dependent code. Debian packagers have written replacement +# make files(!). Either we use these, or negotiate a version which can +# be pushed upstream to NCBI. +# +# Another note: you may want the older and deprecated C-libs at ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/2008/Mar_17_2008/NCBI_C_Toolkit/ncbi_c--Mar_17_2008.tar.gz + +stdenv.mkDerivation rec { + name = "ncbi_tools"; + ncbi_version = "Dec_31_2008"; + src = fetchurl { + url = "ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/2008/${ncbi_version}/ncbi_cxx--${ncbi_version}.tar.gz"; + sha256 = "1b2v0dcdqn3bysgdkj57sxmd6s0hc9wpnxssviz399g6plhxggbr"; + }; + + configureFlags = [ + "--without-debug" + "--with-bin-release" + "--with-dll" + "--without-static" + ]; + buildInputs = [ cpio ]; + + meta = { + description = ''NCBI Bioinformatics toolbox (incl. BLAST)''; + longDescription = ''The NCBI Bioinformatics toolsbox, including command-line utilties, libraries and include files. No X11 support''; + homepage = http://www.ncbi.nlm.nih.gov/IEB/ToolBox/; + license = "GPL"; + priority = 5; # zlib.so gives a conflict with zlib + broken = true; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/neuron/default.nix b/nixpkgs/pkgs/applications/science/biology/neuron/default.nix new file mode 100644 index 000000000000..35710fd1fe1f --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/neuron/default.nix @@ -0,0 +1,80 @@ +{ stdenv +, fetchurl +, pkgconfig +, automake +, autoconf +, libtool +, ncurses +, readline +, which +, python ? null +, mpi ? null +, iv +}: + +stdenv.mkDerivation rec { + name = "neuron-${version}"; + version = "7.5"; + + nativeBuildInputs = [ which pkgconfig automake autoconf libtool ]; + buildInputs = [ ncurses readline python mpi iv ]; + + src = fetchurl { + url = "https://www.neuron.yale.edu/ftp/neuron/versions/v${version}/nrn-${version}.tar.gz"; + sha256 = "0f26v3qvzblcdjg7isq0m9j2q8q7x3vhmkfllv8lsr3gyj44lljf"; + }; + + patches = (stdenv.lib.optional (stdenv.isDarwin) [ ./neuron-carbon-disable.patch ]); + + # With LLVM 3.8 and above, clang (really libc++) gets upset if you attempt to redefine these... + postPatch = stdenv.lib.optionalString stdenv.cc.isClang '' + substituteInPlace src/gnu/neuron_gnu_builtin.h \ + --replace 'double abs(double arg);' "" \ + --replace 'float abs(float arg);' "" \ + --replace 'short abs(short arg);' "" \ + --replace 'long abs(long arg);' "" + ''; + + enableParallelBuilding = true; + + ## neuron install by default everything under prefix/${host_arch}/* + ## override this to support nix standard file hierarchy + ## without issues: install everything under prefix/ + preConfigure = '' + ./build.sh + export prefix="''${prefix} --exec-prefix=''${out}" + ''; + + configureFlags = with stdenv.lib; + [ "--with-readline=${readline}" "--with-iv=${iv}" ] + ++ optionals (python != null) [ "--with-nrnpython=${python.interpreter}" ] + ++ (if mpi != null then ["--with-mpi" "--with-paranrn"] + else ["--without-mpi"]); + + + postInstall = stdenv.lib.optionals (python != null) [ '' + ## standardise python neuron install dir if any + if [[ -d $out/lib/python ]]; then + mkdir -p ''${out}/${python.sitePackages} + mv ''${out}/lib/python/* ''${out}/${python.sitePackages}/ + fi + '']; + + propagatedBuildInputs = [ readline ncurses which libtool ]; + + meta = with stdenv.lib; { + description = "Simulation environment for empirically-based simulations of neurons and networks of neurons"; + + longDescription = "NEURON is a simulation environment for developing and exercising models of + neurons and networks of neurons. It is particularly well-suited to problems where + cable properties of cells play an important role, possibly including extracellular + potential close to the membrane), and where cell membrane properties are complex, + involving many ion-specific channels, ion accumulation, and second messengers"; + + license = licenses.bsd3; + homepage = http://www.neuron.yale.edu/neuron; + maintainers = [ maintainers.adev ]; + platforms = platforms.all; + }; +} + diff --git a/nixpkgs/pkgs/applications/science/biology/neuron/neuron-carbon-disable.patch b/nixpkgs/pkgs/applications/science/biology/neuron/neuron-carbon-disable.patch new file mode 100644 index 000000000000..923bffb1c338 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/neuron/neuron-carbon-disable.patch @@ -0,0 +1,21 @@ +--- nrn-7.4/src/mac/Makefile.am 2015-11-12 21:42:45.000000000 +0100 ++++ nrn-7.4.new/src/mac/Makefile.am 2016-08-24 17:43:39.000000000 +0200 +@@ -15,18 +15,8 @@ + host_cpu = @host_cpu@ + + if MAC_DARWIN +-carbon = @enable_carbon@ + bin_SCRIPTS = $(launch_scripts) + install: install-am +-if UniversalMacBinary +- $(CC) -arch ppc -o aoutppc -Dcpu="\"$(host_cpu)\"" -I. $(srcdir)/launch.c $(srcdir)/mac2uxarg.c -framework Carbon +- $(CC) -arch i386 -o aouti386 -Dcpu="\"$(host_cpu)\"" -I. $(srcdir)/launch.c $(srcdir)/mac2uxarg.c -framework Carbon +- lipo aouti386 aoutppc -create -output a.out +-else +- gcc -g -arch i386 -Dncpu="\"$(host_cpu)\"" -I. $(srcdir)/launch.c $(srcdir)/mac2uxarg.c -framework Carbon +- +-endif +- carbon=$(carbon) sh $(srcdir)/launch_inst.sh "$(host_cpu)" "$(DESTDIR)$(prefix)" "$(srcdir)" + for i in $(S) ; do \ + sed "s/^CPU.*/CPU=\"$(host_cpu)\"/" < $(DESTDIR)$(bindir)/$$i > temp; \ + mv temp $(DESTDIR)$(bindir)/$$i; \ diff --git a/nixpkgs/pkgs/applications/science/biology/niftyreg/default.nix b/nixpkgs/pkgs/applications/science/biology/niftyreg/default.nix new file mode 100644 index 000000000000..9f24046b3bf6 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/niftyreg/default.nix @@ -0,0 +1,24 @@ +{ stdenv, lib, fetchurl, cmake, zlib }: + +stdenv.mkDerivation rec { + pname = "niftyreg"; + version = "1.3.9"; + name = "${pname}-${version}"; + + src = fetchurl { + url = "mirror://sourceforge/${pname}/nifty_reg-${version}/nifty_reg-${version}.tar.gz"; + sha256 = "07v9v9s41lvw72wpb1jgh2nzanyc994779bd35p76vg8mzifmprl"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ zlib ]; + enableParallelBuilding = true; + + meta = with stdenv.lib; { + homepage = http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg; + description = "Medical image registration software"; + maintainers = with maintainers; [ bcdarwin ]; + platforms = [ "x86_64-linux" ]; + license = licenses.bsd3; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/niftyseg/default.nix b/nixpkgs/pkgs/applications/science/biology/niftyseg/default.nix new file mode 100644 index 000000000000..671ee4b95c65 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/niftyseg/default.nix @@ -0,0 +1,24 @@ +{ stdenv, lib, fetchurl, cmake, eigen, zlib }: + +stdenv.mkDerivation rec { + pname = "niftyseg"; + version = "1.0"; + name = "${pname}-${version}"; + src = fetchurl { + url = "https://github.com/KCL-BMEIS/NiftySeg/archive/v${version}.tar.gz"; + sha256 = "11q6yldsxp3k6gfp94c0xhcan2y3finzv8lzizmrc79yps3wjkn0"; + }; + + nativeBuildInputs = [ cmake ]; + buildInputs = [ eigen zlib ]; + enableParallelBuilding = true; + + meta = with stdenv.lib; { + 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; + license = licenses.bsd3; + }; + +} diff --git a/nixpkgs/pkgs/applications/science/biology/paml/default.nix b/nixpkgs/pkgs/applications/science/biology/paml/default.nix new file mode 100644 index 000000000000..fe25a04c420a --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/paml/default.nix @@ -0,0 +1,33 @@ +{stdenv, fetchurl}: + +stdenv.mkDerivation rec { + version = "4.9h"; + name = "paml-${version}"; + src = fetchurl { + url = "http://abacus.gene.ucl.ac.uk/software/paml${version}.tgz"; + sha256 = "1czdfb3naadq0d3y42isrbyja33c3p28k8dv9mxlx2h19b7zcfv2"; + }; + + preBuild = '' + cd ./src/ + ''; + installPhase = '' + mkdir -pv $out/bin + cp -v codeml $out/bin + cp -v baseml $out/bin + cp -v basemlg $out/bin + cp -v chi2 $out/bin + cp -v codeml $out/bin + cp -v evolver $out/bin + cp -v mcmctree $out/bin + cp -v pamp $out/bin + cp -v yn00 $out/bin + ''; + + meta = { + description = "Phylogenetic Analysis by Maximum Likelihood (PAML)"; + longDescription = ''PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc.''; + license = "non-commercial"; + homepage = http://abacus.gene.ucl.ac.uk/software/paml.html; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix new file mode 100644 index 000000000000..2ba5964d6104 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix @@ -0,0 +1,31 @@ +{stdenv, fetchurl, jre, makeWrapper}: + +stdenv.mkDerivation rec { + name = "picard-tools-${version}"; + version = "2.18.25"; + + src = fetchurl { + url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; + sha256 = "03d3mnf3gddngn3dhwb00v8k40x6ncgprn22w4vyfr96917p2snx"; + }; + + nativeBuildInputs = [ makeWrapper ]; + buildInputs = [ jre ]; + + 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 $out/libexec/picard/picard.jar" + ''; + + meta = with stdenv.lib; { + description = "Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF"; + license = licenses.mit; + homepage = https://broadinstitute.github.io/picard/; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.all; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/platypus/default.nix b/nixpkgs/pkgs/applications/science/biology/platypus/default.nix new file mode 100644 index 000000000000..323ca90f0a2a --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/platypus/default.nix @@ -0,0 +1,38 @@ +{stdenv, fetchFromGitHub, python27, htslib, zlib, makeWrapper}: + +let python = python27.withPackages (ps: with ps; [ cython ]); + +in stdenv.mkDerivation rec { + name = "platypus-unstable-${version}"; + version = "2018-07-22"; + + src = fetchFromGitHub { + owner = "andyrimmer"; + repo = "Platypus"; + rev = "3e72641c69800da0cd4906b090298e654d316ee1"; + sha256 = "0nah6r54b8xm778gqyb8b7rsd76z8ji4g73sm6rvpw5s96iib1vw"; + }; + + 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.x86_64; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/plink-ng/default.nix b/nixpkgs/pkgs/applications/science/biology/plink-ng/default.nix new file mode 100644 index 000000000000..2efb59f536f6 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/plink-ng/default.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchFromGitHub, zlib, openblas, darwin}: + +stdenv.mkDerivation rec { + name = "plink-ng-${version}"; + version = "1.90b3"; + + src = fetchFromGitHub { + owner = "chrchang"; + repo = "plink-ng"; + rev = "v${version}"; + sha256 = "1zhffjbwpd50dxywccbnv1rxy9njwz73l4awc5j7i28rgj3davcq"; + }; + + buildInputs = [ zlib ] ++ (if stdenv.isDarwin then [ darwin.apple_sdk.frameworks.Accelerate ] else [ openblas ]) ; + + buildPhase = '' + sed -i 's|zlib-1.2.8/zlib.h|zlib.h|g' *.c *.h + ${if stdenv.cc.isClang then "sed -i 's|g++|clang++|g' Makefile.std" else ""} + make ZLIB=-lz ${if stdenv.isDarwin then "" else "BLASFLAGS=-lopenblas"} -f Makefile.std + ''; + + installPhase = '' + mkdir -p $out/bin + cp plink $out/bin + ''; + + meta = { + description = "A comprehensive update to the PLINK association analysis toolset"; + homepage = https://www.cog-genomics.org/plink2; + license = stdenv.lib.licenses.gpl3; + platforms = stdenv.lib.platforms.linux; + }; +} + diff --git a/nixpkgs/pkgs/applications/science/biology/plink/default.nix b/nixpkgs/pkgs/applications/science/biology/plink/default.nix new file mode 100644 index 000000000000..cc48a0cb13a9 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/plink/default.nix @@ -0,0 +1,25 @@ +{ 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 $out/bin + ''; + + meta = { + description = "Whole genome association toolkit"; + homepage = http://pngu.mgh.harvard.edu/~purcell/plink/; + license = stdenv.lib.licenses.gpl2; + platforms = stdenv.lib.platforms.all; + broken = true; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/poretools/default.nix b/nixpkgs/pkgs/applications/science/biology/poretools/default.nix new file mode 100755 index 000000000000..3bb9ea06fd46 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/poretools/default.nix @@ -0,0 +1,23 @@ +{ stdenv, pythonPackages, fetchFromGitHub }: + +pythonPackages.buildPythonPackage rec { + pname = "poretools"; + version = "unstable-2016-07-10"; + name = "${pname}-${version}"; + + src = fetchFromGitHub { + repo = pname; + owner = "arq5x"; + rev = "e426b1f09e86ac259a00c261c79df91510777407"; + sha256 = "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am"; + }; + + propagatedBuildInputs = [pythonPackages.h5py pythonPackages.matplotlib pythonPackages.seaborn pythonPackages.pandas]; + + meta = { + description = "a toolkit for working with nanopore sequencing data from Oxford Nanopore"; + license = stdenv.lib.licenses.mit; + homepage = http://poretools.readthedocs.io/en/latest/; + maintainers = [stdenv.lib.maintainers.rybern]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/raxml/default.nix b/nixpkgs/pkgs/applications/science/biology/raxml/default.nix new file mode 100644 index 000000000000..140f70323194 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/raxml/default.nix @@ -0,0 +1,41 @@ +{ stdenv +, fetchFromGitHub +, pkgs +, mpi ? false +}: + +stdenv.mkDerivation rec { + pname = "RAxML"; + version = "8.2.12"; + name = "${pname}-${version}"; + + src = fetchFromGitHub { + owner = "stamatak"; + repo = "standard-${pname}"; + rev = "v${version}"; + sha256 = "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh"; + }; + + buildInputs = if mpi then [ pkgs.openmpi ] else []; + + # TODO darwin, AVX and AVX2 makefile targets + buildPhase = if mpi then '' + make -f Makefile.MPI.gcc + '' else '' + make -f Makefile.SSE3.PTHREADS.gcc + ''; + + installPhase = if mpi then '' + mkdir -p $out/bin && cp raxmlHPC-MPI $out/bin + '' else '' + mkdir -p $out/bin && cp raxmlHPC-PTHREADS-SSE3 $out/bin + ''; + + meta = with stdenv.lib; { + description = "A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies"; + license = licenses.gpl3; + homepage = https://sco.h-its.org/exelixis/web/software/raxml/; + maintainers = [ maintainers.unode ]; + platforms = [ "i686-linux" "x86_64-linux" ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/samtools/default.nix b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix new file mode 100644 index 000000000000..c4b4bb522c40 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix @@ -0,0 +1,35 @@ +{ stdenv, fetchurl, zlib, htslib, perl, ncurses ? null }: + +stdenv.mkDerivation rec { + name = "${pname}-${version}"; + pname = "samtools"; + version = "1.9"; + + src = fetchurl { + url = "https://github.com/samtools/samtools/releases/download/${version}/${name}.tar.bz2"; + sha256 = "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8"; + }; + + nativeBuildInputs = [ perl ]; + + buildInputs = [ zlib ncurses htslib ]; + + configureFlags = [ "--with-htslib=${htslib}" ] + ++ stdenv.lib.optional (ncurses == null) "--without-curses"; + + preCheck = '' + patchShebangs test/ + ''; + + enableParallelBuilding = true; + + doCheck = true; + + meta = with stdenv.lib; { + description = "Tools for manipulating SAM/BAM/CRAM format"; + license = licenses.mit; + homepage = http://www.htslib.org/; + platforms = platforms.unix; + maintainers = [ maintainers.mimadrid ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch b/nixpkgs/pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch new file mode 100644 index 000000000000..a7782a1a0264 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/samtools/samtools-0.1.19-no-curses.patch @@ -0,0 +1,22 @@ +diff --git a/Makefile b/Makefile +index 2f51bfc..395d6f1 100644 +--- a/Makefile ++++ b/Makefile +@@ -1,7 +1,7 @@ + CC= gcc + CFLAGS= -g -Wall -O2 + #LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib +-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 ++DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE # -D_CURSES_LIB=1 + KNETFILE_O= knetfile.o + LOBJS= bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o \ + bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \ +@@ -15,7 +15,7 @@ PROG= samtools + INCLUDES= -I. + SUBDIRS= . bcftools misc + LIBPATH= +-LIBCURSES= -lcurses # -lXCurses ++LIBCURSES= # -lcurses # -lXCurses + + .SUFFIXES:.c .o + .PHONY: all lib diff --git a/nixpkgs/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix b/nixpkgs/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix new file mode 100644 index 000000000000..a811bc4412f2 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchurl, zlib }: + +stdenv.mkDerivation rec { + name = "${pname}-${version}"; + pname = "samtools"; + version = "0.1.19"; + + src = fetchurl { + url = "mirror://sourceforge/samtools/${name}.tar.bz2"; + sha256 = "d080c9d356e5f0ad334007e4461cbcee3c4ca97b8a7a5a48c44883cf9dee63d4"; + }; + + patches = [ + ./samtools-0.1.19-no-curses.patch + ]; + + buildInputs = [ zlib ]; + + installPhase = '' + mkdir -p $out/bin + mkdir -p $out/share/man + + cp samtools $out/bin + cp samtools.1 $out/share/man + ''; + + meta = with stdenv.lib; { + description = "Tools for manipulating SAM/BAM/CRAM format"; + license = licenses.mit; + homepage = http://samtools.sourceforge.net/; + platforms = platforms.unix; + maintainers = [ maintainers.unode ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/seaview/default.nix b/nixpkgs/pkgs/applications/science/biology/seaview/default.nix new file mode 100644 index 000000000000..17cf903ae49c --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/seaview/default.nix @@ -0,0 +1,41 @@ +{ stdenv, fetchurl, coreutils, fltk, libjpeg }: + +stdenv.mkDerivation rec { + version = "4.7"; + name = "seaview-${version}"; + + src = fetchurl { + url = "ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/archive/seaview_${version}.tar.gz"; + sha256 = "0fhyq7dcn0izhwcfin9ajsr7kmmsqm9f1np1rmhzg4digfwqb29n"; + }; + + buildInputs = [ fltk libjpeg ]; + + patchPhase = "sed -i 's#PATH=/bin:/usr/bin rm#'${coreutils}/bin/rm'#' seaview.cxx"; + installPhase = "mkdir -p $out/bin; cp seaview $out/bin"; + + meta = with stdenv.lib; { + description = "GUI for molecular phylogeny"; + longDescription = '' + SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. + - SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. + - SeaView drives programs muscle or Clustal Omega for multiple sequence alignment, and also allows to use any external alignment algorithm able to read and write FASTA-formatted files. + - Seaview drives the Gblocks program to select blocks of evolutionarily conserved sites. + - SeaView computes phylogenetic trees by + + parsimony, using PHYLIP's dnapars/protpars algorithm, + + distance, with NJ or BioNJ algorithms on a variety of evolutionary distances, + + maximum likelihood, driving program PhyML 3.1. + - Seaview can use the Transfer Bootstrap Expectation method to compute the bootstrap support of PhyML and distance trees. + - SeaView prints and draws phylogenetic trees on screen, SVG, PDF or PostScript files. + - SeaView allows to download sequences from EMBL/GenBank/UniProt using the Internet. + + Seaview is published in: + + Gouy M., Guindon S. & Gascuel O. (2010) SeaView version 4 : a multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Molecular Biology and Evolution 27(2):221-224. + ''; + homepage = http://doua.prabi.fr/software/seaview; + license = licenses.gpl3; + maintainers = [ maintainers.iimog ]; + platforms = platforms.linux; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix b/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix new file mode 100644 index 000000000000..dc2246903349 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/snpeff/default.nix @@ -0,0 +1,33 @@ +{stdenv, fetchurl, jre, unzip, makeWrapper}: + +stdenv.mkDerivation rec { + name = "snpeff-${version}"; + version = "4.3t"; + + src = fetchurl { + url = "mirror://sourceforge/project/snpeff/snpEff_v${builtins.replaceStrings [ "." ] [ "_" ] version}_core.zip"; + sha256 = "0i12mv93bfv8xjwc3rs2x73d6hkvi7kgbbbx3ry984l3ly4p6nnm"; + }; + + buildInputs = [ unzip jre makeWrapper ]; + + sourceRoot = "snpEff"; + + 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 $out/libexec/snpeff/SnpSift.jar" + ''; + + meta = with stdenv.lib; { + description = "Genetic variant annotation and effect prediction toolbox."; + license = licenses.lgpl3; + homepage = http://snpeff.sourceforge.net/; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.all; + }; + +} diff --git a/nixpkgs/pkgs/applications/science/biology/somatic-sniper/default.nix b/nixpkgs/pkgs/applications/science/biology/somatic-sniper/default.nix new file mode 100644 index 000000000000..4bbd6a320035 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/somatic-sniper/default.nix @@ -0,0 +1,28 @@ +{stdenv, fetchFromGitHub, cmake, zlib, ncurses}: + +stdenv.mkDerivation rec { + name = "somatic-sniper-${version}"; + version = "1.0.5.0"; + + src = fetchFromGitHub { + owner = "genome"; + repo = "somatic-sniper"; + rev = "v${version}"; + sha256 = "0lk7p9sp6mp50f6w1nppqhr40fcwy1asw06ivw8w8jvvnwaqf987"; + }; + + patches = [ ./somatic-sniper.patch ]; + + buildInputs = [ cmake zlib ncurses ]; + + enableParallelBuilding = false; + + meta = with stdenv.lib; { + description = "Identify single nucleotide positions that are different between tumor and normal"; + license = licenses.mit; + homepage = https://github.com/genome/somatic-sniper; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.linux; + }; + +} diff --git a/nixpkgs/pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch b/nixpkgs/pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch new file mode 100644 index 000000000000..9af04c0a0696 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/somatic-sniper/somatic-sniper.patch @@ -0,0 +1,26 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 6d5a180..7254292 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -11,7 +11,7 @@ set(CMAKE_MODULE_PATH + ) + + include(TestHelper) +-include(VersionHelper) ++#include(VersionHelper) + include(ProjectHelper) + + # NOTE: for sniper we want the exe suffix to be like 0.7.4, not just 0.7 +diff --git a/vendor/samtools.patch b/vendor/samtools.patch +index f173017..654f878 100644 +--- a/vendor/samtools.patch ++++ b/vendor/samtools.patch +@@ -6,7 +6,7 @@ diff -Nuar a/Makefile b/Makefile + + samtools:lib $(AOBJS) + - $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -lz -L. -lbam +-+ $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) $(LIBCURSES) -L. -lbam -lz +++ $(CC) $(CFLAGS) -o $@ $(AOBJS) -lm $(LIBPATH) -lncurses -L. -lbam -lz + + razip:razip.o razf.o + $(CC) $(CFLAGS) -o $@ razf.o razip.o -lz diff --git a/nixpkgs/pkgs/applications/science/biology/star/default.nix b/nixpkgs/pkgs/applications/science/biology/star/default.nix new file mode 100644 index 000000000000..eb62a8c331f8 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/star/default.nix @@ -0,0 +1,34 @@ +{ stdenv, fetchFromGitHub, zlib }: + +stdenv.mkDerivation rec { + name = "star-${version}"; + version = "2.7.0c"; + + src = fetchFromGitHub { + repo = "STAR"; + owner = "alexdobin"; + rev = version; + sha256 = "0r5jcckr45f71jwhz8xazi1w6kfhszq3y6r7f6zl9963ms1q1gfv"; + }; + + sourceRoot = "source/source"; + + postPatch = "sed 's:/bin/rm:rm:g' -i Makefile"; + + buildInputs = [ zlib ]; + + buildPhase = "make STAR STARlong"; + + installPhase = '' + mkdir -p $out/bin + cp STAR STARlong $out/bin + ''; + + meta = with stdenv.lib; { + description = "Spliced Transcripts Alignment to a Reference"; + homepage = https://github.com/alexdobin/STAR; + license = licenses.gpl3Plus; + platforms = platforms.linux; + maintainers = [ maintainers.arcadio ]; + }; +} diff --git a/nixpkgs/pkgs/applications/science/biology/strelka/default.nix b/nixpkgs/pkgs/applications/science/biology/strelka/default.nix new file mode 100644 index 000000000000..1527f5d3ddad --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/strelka/default.nix @@ -0,0 +1,37 @@ +{stdenv, fetchFromGitHub, cmake, zlib, python2}: + +stdenv.mkDerivation rec { + name = "strelka-${version}"; + version = "2.9.5"; + + src = fetchFromGitHub { + owner = "Illumina"; + repo = "strelka"; + rev = "v${version}"; + sha256 = "0x4a6nkx1jnyag9svghsdjz1fz6q7qx5pn77wphdfnk81f9yspf8"; + }; + + buildInputs = [ cmake zlib python2 ]; + + preConfigure = '' + sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py + patchShebangs . + ''; + + postFixup = '' + pushd $out/lib/python/pyflow + sed -i 's|/bin/bash|${stdenv.shell}|' pyflowTaskWrapper.py + rm pyflowTaskWrapper.pyc + echo "import pyflowTaskWrapper" | python2 + popd + ''; + + meta = with stdenv.lib; { + description = "Germline and small variant caller"; + license = licenses.gpl3; + homepage = https://github.com/Illumina/strelka; + maintainers = with maintainers; [ jbedo ]; + platforms = [ "x86_64-linux" ]; + }; + +} diff --git a/nixpkgs/pkgs/applications/science/biology/varscan/default.nix b/nixpkgs/pkgs/applications/science/biology/varscan/default.nix new file mode 100644 index 000000000000..f685031e87e4 --- /dev/null +++ b/nixpkgs/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 $out/libexec/varscan/varscan.jar" + ''; + + meta = with stdenv.lib; { + description = "Variant calling and somatic mutation/CNV detection for next-generation sequencing data"; + # VarScan 2 is free for non-commercial use by academic, + # government, and non-profit/not-for-profit institutions. A + # commercial version of the software is available, and licensed + # through the Office of Technology Management at Washington + # University School of Medicine. + license = licenses.unfree; + homepage = https://github.com/dkoboldt/varscan; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.all; + }; + +} diff --git a/nixpkgs/pkgs/applications/science/biology/vcftools/default.nix b/nixpkgs/pkgs/applications/science/biology/vcftools/default.nix new file mode 100755 index 000000000000..a6f52ae97b59 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/vcftools/default.nix @@ -0,0 +1,24 @@ +{ stdenv, fetchFromGitHub, zlib, autoreconfHook, pkgconfig, perl }: + +stdenv.mkDerivation rec { + name = "${pname}-${version}"; + pname = "vcftools"; + version = "0.1.16"; + + src = fetchFromGitHub { + repo = pname; + owner = "vcftools"; + rev = "v${version}"; + sha256 = "0msb09d2cnm8rlpg8bsc1lhjddvp3kf3i9dsj1qs4qgsdlzhxkyx"; + }; + + buildInputs = [ autoreconfHook pkgconfig zlib perl ]; + + meta = with stdenv.lib; { + description = "A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project"; + license = licenses.lgpl3; + platforms = platforms.linux; + homepage = https://vcftools.github.io/index.html; + maintainers = [ maintainers.rybern ]; + }; +} |