diff options
Diffstat (limited to 'pkgs/applications/science/biology')
72 files changed, 142 insertions, 142 deletions
diff --git a/pkgs/applications/science/biology/EZminc/default.nix b/pkgs/applications/science/biology/EZminc/default.nix index f9d3e4d4e1279..17d8944128e2d 100644 --- a/pkgs/applications/science/biology/EZminc/default.nix +++ b/pkgs/applications/science/biology/EZminc/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, pkgconfig, libminc, bicpl, itk4, fftwFloat, gsl }: +{ lib, stdenv, fetchFromGitHub, cmake, pkgconfig, libminc, bicpl, itk4, fftwFloat, gsl }: stdenv.mkDerivation rec { pname = "EZminc"; @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { "-DEZMINC_BUILD_MRFSEG=TRUE" "-DEZMINC_BUILD_DD=TRUE" ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/BIC-MNI/${pname}"; description = "Collection of Perl and shell scripts for processing MINC files"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/pkgs/applications/science/biology/N3/default.nix b/pkgs/applications/science/biology/N3/default.nix index 13ffc305d3926..2f4aa4ce3927e 100644 --- a/pkgs/applications/science/biology/N3/default.nix +++ b/pkgs/applications/science/biology/N3/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, makeWrapper, +{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, libminc, EBTKS }: @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { done ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/BIC-MNI/N3"; description = "MRI non-uniformity correction for MINC files"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/pkgs/applications/science/biology/ants/default.nix b/pkgs/applications/science/biology/ants/default.nix index caf759ce7e3f4..7aa41bdf6f04a 100644 --- a/pkgs/applications/science/biology/ants/default.nix +++ b/pkgs/applications/science/biology/ants/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, itk4, vtk_7, Cocoa }: +{ lib, stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, itk4, vtk_7, Cocoa }: stdenv.mkDerivation rec { pname = "ANTs"; @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { done ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/ANTsX/ANTs"; description = "Advanced normalization toolkit for medical image registration and other processing"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/pkgs/applications/science/biology/aragorn/default.nix b/pkgs/applications/science/biology/aragorn/default.nix index 168bd5c6aa683..fa0c10b00c205 100644 --- a/pkgs/applications/science/biology/aragorn/default.nix +++ b/pkgs/applications/science/biology/aragorn/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl }: +{ lib, stdenv, fetchurl }: stdenv.mkDerivation rec { version = "1.2.38"; @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { mkdir -p $out/man/1 && cp aragorn.1 $out/man/1 ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Detects tRNA, mtRNA, and tmRNA genes in nucleotide sequences"; homepage = "http://mbio-serv2.mbioekol.lu.se/ARAGORN/"; license = licenses.gpl2; diff --git a/pkgs/applications/science/biology/bayescan/default.nix b/pkgs/applications/science/biology/bayescan/default.nix index 4e216fbdbe63f..7c4f198b8427a 100644 --- a/pkgs/applications/science/biology/bayescan/default.nix +++ b/pkgs/applications/science/biology/bayescan/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, unzip, llvmPackages }: +{ lib, stdenv, fetchurl, unzip, llvmPackages }: stdenv.mkDerivation rec { pname = "bayescan"; @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { cp -r ../*pdf ../input_examples ../"R functions" $out/share/doc/bayescan ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Detecting natural selection from population-based genetic data"; homepage = "http://cmpg.unibe.ch/software/BayeScan"; license = licenses.gpl3; diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix index d1b033dc4e23f..f4e2db01fbc56 100644 --- a/pkgs/applications/science/biology/bcftools/default.nix +++ b/pkgs/applications/science/biology/bcftools/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, python, bash }: +{ lib, stdenv, fetchurl, htslib, zlib, bzip2, lzma, curl, perl, python, bash }: stdenv.mkDerivation rec { pname = "bcftools"; @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { doCheck = true; - meta = with stdenv.lib; { + meta = with lib; { description = "Tools for manipulating BCF2/VCF/gVCF format, SNP and short indel sequence variants"; license = licenses.mit; homepage = "http://www.htslib.org/"; diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix index f92e912f6800e..cfa22ae5ac8be 100644 --- a/pkgs/applications/science/biology/bedtools/default.nix +++ b/pkgs/applications/science/biology/bedtools/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchFromGitHub, zlib, python, bzip2, lzma}: +{lib, stdenv, fetchFromGitHub, zlib, python, bzip2, lzma}: stdenv.mkDerivation rec { pname = "bedtools"; @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} -j $NIX_BUILD_CORES"; installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} install"; - meta = with stdenv.lib; { + meta = with lib; { description = "A powerful toolset for genome arithmetic"; license = licenses.gpl2; homepage = "https://bedtools.readthedocs.io/en/latest/"; diff --git a/pkgs/applications/science/biology/bftools/default.nix b/pkgs/applications/science/biology/bftools/default.nix index 2ecefee340fd6..89ebdcee65b92 100644 --- a/pkgs/applications/science/biology/bftools/default.nix +++ b/pkgs/applications/science/biology/bftools/default.nix @@ -31,7 +31,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ makeWrapper ]; - meta = with stdenv.lib; { + meta = with lib; { description = "A bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already included"; license = licenses.gpl2; platforms = platforms.all; diff --git a/pkgs/applications/science/biology/blast/default.nix b/pkgs/applications/science/biology/blast/default.nix index 95a1b905e9e24..a72f16938d410 100644 --- a/pkgs/applications/science/biology/blast/default.nix +++ b/pkgs/applications/science/biology/blast/default.nix @@ -94,7 +94,7 @@ stdenv.mkDerivation rec { # Many tests require either network access or locally available databases doCheck = false; - meta = with stdenv.lib; { + meta = with lib; { description = ''Basic Local Alignment Search Tool (BLAST) finds regions of similarity between biological sequences''; homepage = "https://blast.ncbi.nlm.nih.gov/Blast.cgi"; diff --git a/pkgs/applications/science/biology/bowtie/default.nix b/pkgs/applications/science/biology/bowtie/default.nix index 964eeddb461da..916bba5c05124 100644 --- a/pkgs/applications/science/biology/bowtie/default.nix +++ b/pkgs/applications/science/biology/bowtie/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, zlib }: +{ lib, stdenv, fetchFromGitHub, zlib }: stdenv.mkDerivation rec { pname = "bowtie"; @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { installFlags = [ "prefix=$(out)" ]; - meta = with stdenv.lib; { + meta = with lib; { description = "An ultrafast memory-efficient short read aligner"; license = licenses.artistic2; homepage = "http://bowtie-bio.sf.net/bowtie"; diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix index 603e5892ff119..715f5bb8bfa68 100644 --- a/pkgs/applications/science/biology/bowtie2/default.nix +++ b/pkgs/applications/science/biology/bowtie2/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, tbb, zlib }: +{ lib, stdenv, fetchFromGitHub, cmake, tbb, zlib }: stdenv.mkDerivation rec { pname = "bowtie2"; @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { buildInputs = [ tbb zlib ]; - meta = with stdenv.lib; { + meta = with 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"; diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix index 10859d9e8c138..a2a11b1d4517f 100644 --- a/pkgs/applications/science/biology/bwa/default.nix +++ b/pkgs/applications/science/biology/bwa/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, zlib }: +{ lib, stdenv, fetchurl, zlib }: stdenv.mkDerivation rec { pname = "bwa"; @@ -28,7 +28,7 @@ stdenv.mkDerivation rec { install -vD -t $out/include bwt.h ''; - meta = with stdenv.lib; { + meta = with 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/"; diff --git a/pkgs/applications/science/biology/cd-hit/default.nix b/pkgs/applications/science/biology/cd-hit/default.nix index 0db788b0f7431..94012b1c2ff44 100644 --- a/pkgs/applications/science/biology/cd-hit/default.nix +++ b/pkgs/applications/science/biology/cd-hit/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, makeWrapper, zlib, perl, perlPackages }: +{ lib, stdenv, fetchFromGitHub, makeWrapper, zlib, perl, perlPackages }: stdenv.mkDerivation rec { version = "4.8.1"; @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { wrapProgram $out/bin/plot_2d.pl --prefix PERL5LIB : $PERL5LIB wrapProgram $out/bin/clstr_list_sort.pl --prefix PERL5LIB : $PERL5LIB ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Clustering and comparing protein or nucleotide sequences"; homepage = "http://weizhongli-lab.org/cd-hit/"; license = licenses.gpl2; diff --git a/pkgs/applications/science/biology/clustal-omega/default.nix b/pkgs/applications/science/biology/clustal-omega/default.nix index 71cf879853767..6377e1fce855d 100644 --- a/pkgs/applications/science/biology/clustal-omega/default.nix +++ b/pkgs/applications/science/biology/clustal-omega/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, argtable }: +{ lib, stdenv, fetchurl, argtable }: stdenv.mkDerivation rec { version = "1.2.4"; @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { done ''; - meta = with stdenv.lib; { + meta = with lib; { description = "General purpose multiple sequence alignment program for protein and DNA/RNA"; homepage = "http://www.clustal.org/omega/"; license = licenses.gpl2; diff --git a/pkgs/applications/science/biology/cmtk/default.nix b/pkgs/applications/science/biology/cmtk/default.nix index 7aef4c0728193..ea4f55ba475a5 100644 --- a/pkgs/applications/science/biology/cmtk/default.nix +++ b/pkgs/applications/science/biology/cmtk/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchurl, cmake}: +{lib, stdenv, fetchurl, cmake}: stdenv.mkDerivation { name = "cmtk-3.3.1"; @@ -13,7 +13,7 @@ stdenv.mkDerivation { NIX_CFLAGS_COMPILE = stdenv.lib.optionalString stdenv.cc.isClang "-Wno-error=c++11-narrowing"; - meta = with stdenv.lib; { + meta = with 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 diff --git a/pkgs/applications/science/biology/conglomerate/default.nix b/pkgs/applications/science/biology/conglomerate/default.nix index 8fb8e17eef860..592ab2cd66332 100644 --- a/pkgs/applications/science/biology/conglomerate/default.nix +++ b/pkgs/applications/science/biology/conglomerate/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, coreutils, perlPackages, bicpl, libminc, zlib, minc_tools, +{ lib, stdenv, fetchFromGitHub, cmake, coreutils, perlPackages, bicpl, libminc, zlib, minc_tools, makeWrapper }: stdenv.mkDerivation rec { @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { done ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/BIC-MNI/conglomerate"; description = "More command-line utilities for working with MINC files"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix index a59e5d2be2d5d..7ec5476cb8261 100644 --- a/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/pkgs/applications/science/biology/dcm2niix/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , cmake , libyamlcpp @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake git ]; buildInputs = [ libyamlcpp ]; - meta = with stdenv.lib; { + meta = with lib; { description = "DICOM to NIfTI converter"; longDescription = '' dcm2niix is a designed to convert neuroimaging data from the diff --git a/pkgs/applications/science/biology/delly/default.nix b/pkgs/applications/science/biology/delly/default.nix index 8f4dd77452692..7a7e3f13c7a3c 100644 --- a/pkgs/applications/science/biology/delly/default.nix +++ b/pkgs/applications/science/biology/delly/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchpatch, fetchFromGitHub, htslib, zlib, bzip2, lzma, ncurses, boost }: +{ lib, stdenv, fetchpatch, fetchFromGitHub, htslib, zlib, bzip2, lzma, ncurses, boost }: stdenv.mkDerivation rec { pname = "delly"; @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { runHook postInstall ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Structural variant caller for mapped DNA sequenced data"; license = licenses.bsd3; maintainers = with maintainers; [ scalavision ]; diff --git a/pkgs/applications/science/biology/diamond/default.nix b/pkgs/applications/science/biology/diamond/default.nix index dd1e13ec7162e..2e11c1d8c58cb 100644 --- a/pkgs/applications/science/biology/diamond/default.nix +++ b/pkgs/applications/science/biology/diamond/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, cmake, zlib }: +{ lib, stdenv, fetchurl, cmake, zlib }: stdenv.mkDerivation { name = "diamond-0.8.36"; @@ -15,7 +15,7 @@ stdenv.mkDerivation { nativeBuildInputs = [ cmake ]; buildInputs = [ zlib ]; - meta = with stdenv.lib; { + meta = with lib; { description = "Accelerated BLAST compatible local sequence aligner"; longDescription = '' A sequence aligner for protein and translated DNA diff --git a/pkgs/applications/science/biology/ecopcr/default.nix b/pkgs/applications/science/biology/ecopcr/default.nix index 2e744c7b2b9ee..b3029f586add4 100644 --- a/pkgs/applications/science/biology/ecopcr/default.nix +++ b/pkgs/applications/science/biology/ecopcr/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, gcc, zlib, python27 }: +{ lib, stdenv, fetchurl, gcc, zlib, python27 }: stdenv.mkDerivation rec { name = "ecopcr-0.8.0"; @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { chmod a+x $out/bin/ecoPCRFormat ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Electronic PCR software tool"; longDescription = '' ecoPCR is an electronic PCR software developed by the LECA. It diff --git a/pkgs/applications/science/biology/eggnog-mapper/default.nix b/pkgs/applications/science/biology/eggnog-mapper/default.nix index 3ef52e543933b..c6defb245c7f9 100644 --- a/pkgs/applications/science/biology/eggnog-mapper/default.nix +++ b/pkgs/applications/science/biology/eggnog-mapper/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, fetchpatch, makeWrapper, python27Packages, wget, diamond, hmmer }: +{ lib, stdenv, fetchFromGitHub, fetchpatch, makeWrapper, python27Packages, wget, diamond, hmmer }: python27Packages.buildPythonApplication rec { pname = "eggnog-mapper"; @@ -30,7 +30,7 @@ python27Packages.buildPythonApplication rec { # the user can download only those that interest them. doCheck = false; - meta = with stdenv.lib; { + meta = with lib; { description = "Fast genome-wide functional annotation through orthology assignment"; license = licenses.gpl2; homepage = "https://github.com/eggnogdb/eggnog-mapper/wiki"; diff --git a/pkgs/applications/science/biology/est-sfs/default.nix b/pkgs/applications/science/biology/est-sfs/default.nix index 1b15c06c670a1..814baa45d8c13 100644 --- a/pkgs/applications/science/biology/est-sfs/default.nix +++ b/pkgs/applications/science/biology/est-sfs/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, gsl }: +{ lib, stdenv, fetchurl, gsl }: stdenv.mkDerivation rec { pname = "est-sfs"; @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { cp est-sfs-documentation.pdf $out/share/doc/${pname} ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://sourceforge.net/projects/est-usfs"; description = "Estimate the unfolded site frequency spectrum and ancestral states"; license = licenses.gpl3; diff --git a/pkgs/applications/science/biology/exonerate/default.nix b/pkgs/applications/science/biology/exonerate/default.nix index b2c49ab007676..9f87d0117df59 100644 --- a/pkgs/applications/science/biology/exonerate/default.nix +++ b/pkgs/applications/science/biology/exonerate/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, glib, pkgconfig }: +{ lib, stdenv, fetchurl, glib, pkgconfig }: stdenv.mkDerivation rec { version = "2.4.0"; @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ pkgconfig ]; - meta = with stdenv.lib; { + meta = with lib; { description = "Generic tool for sequence alignment"; homepage = "https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate"; license = licenses.gpl3; diff --git a/pkgs/applications/science/biology/fastp/default.nix b/pkgs/applications/science/biology/fastp/default.nix index c68486dbcd6be..e396c8597d24b 100644 --- a/pkgs/applications/science/biology/fastp/default.nix +++ b/pkgs/applications/science/biology/fastp/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , zlib }: @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { install -D fastp $out/bin/fastp ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Ultra-fast all-in-one FASTQ preprocessor"; license = licenses.mit; homepage = "https://github.com/OpenGene/fastp"; diff --git a/pkgs/applications/science/biology/freebayes/default.nix b/pkgs/applications/science/biology/freebayes/default.nix index bd80df56cb905..32ab614b9682e 100644 --- a/pkgs/applications/science/biology/freebayes/default.nix +++ b/pkgs/applications/science/biology/freebayes/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, zlib, bzip2, lzma }: +{ lib, stdenv, fetchFromGitHub, zlib, bzip2, lzma }: stdenv.mkDerivation rec { pname = "freebayes"; @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { install -vD bin/freebayes bin/bamleftalign scripts/* -t $out/bin ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Bayesian haplotype-based polymorphism discovery and genotyping"; license = licenses.mit; homepage = "https://github.com/ekg/freebayes"; diff --git a/pkgs/applications/science/biology/hisat2/default.nix b/pkgs/applications/science/biology/hisat2/default.nix index e641489b86c9b..ab8e26f92a0de 100644 --- a/pkgs/applications/science/biology/hisat2/default.nix +++ b/pkgs/applications/science/biology/hisat2/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchFromGitHub, unzip, which, python3, perl}: +{lib, stdenv, fetchFromGitHub, unzip, which, python3, perl}: stdenv.mkDerivation rec { pname = "hisat2"; @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { $out/bin ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Graph based aligner"; license = licenses.gpl3; homepage = "https://ccb.jhu.edu/software/hisat2/index.shtml"; diff --git a/pkgs/applications/science/biology/hmmer/default.nix b/pkgs/applications/science/biology/hmmer/default.nix index 3b1420a18819c..0f83178626bf6 100644 --- a/pkgs/applications/science/biology/hmmer/default.nix +++ b/pkgs/applications/science/biology/hmmer/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl }: +{ lib, stdenv, fetchurl }: stdenv.mkDerivation rec { version = "3.3.2"; @@ -9,7 +9,7 @@ stdenv.mkDerivation rec { sha256 = "0s9wf6n0qanbx8qs6igfl3vyjikwbrvh4d9d6mv54yp3xysykzlj"; }; - meta = with stdenv.lib; { + meta = with 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). diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index 3f9cb1a288b37..ff05ef4b8df61 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchzip, jdk11 }: +{ lib, stdenv, fetchzip, jdk11 }: stdenv.mkDerivation rec { pname = "igv"; @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { chmod +x $out/bin/igvtools ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://www.broadinstitute.org/igv/"; description = "A visualization tool for interactive exploration of genomic datasets"; license = licenses.mit; diff --git a/pkgs/applications/science/biology/inormalize/default.nix b/pkgs/applications/science/biology/inormalize/default.nix index e6293bb90ef38..8ea115c6b25df 100644 --- a/pkgs/applications/science/biology/inormalize/default.nix +++ b/pkgs/applications/science/biology/inormalize/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, makeWrapper, +{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, libminc, EBTKS }: @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { done ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/BIC-MNI/${pname}"; description = "Program to normalize intensity of MINC files"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/pkgs/applications/science/biology/itsx/default.nix b/pkgs/applications/science/biology/itsx/default.nix index 6f66cfc9cc370..843f0df57924b 100644 --- a/pkgs/applications/science/biology/itsx/default.nix +++ b/pkgs/applications/science/biology/itsx/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, hmmer, perl }: +{ lib, stdenv, fetchurl, hmmer, perl }: stdenv.mkDerivation rec { version = "1.1.1"; @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { cp -r ITSx_db $out/share ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing"; homepage = "https://microbiology.se/software/itsx/"; license = licenses.gpl3; diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix index 014ae14cc7948..203d0520660f0 100644 --- a/pkgs/applications/science/biology/kallisto/default.nix +++ b/pkgs/applications/science/biology/kallisto/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, autoconf, cmake, hdf5, zlib }: +{ lib, stdenv, fetchFromGitHub, autoconf, cmake, hdf5, zlib }: stdenv.mkDerivation rec { pname = "kallisto"; @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { # Parallel build fails in some cases: https://github.com/pachterlab/kallisto/issues/160 enableParallelBuilding = false; - meta = with stdenv.lib; { + meta = with lib; { description = "Program for quantifying abundances of transcripts from RNA-Seq data"; homepage = "https://pachterlab.github.io/kallisto"; license = licenses.bsd2; diff --git a/pkgs/applications/science/biology/kent/default.nix b/pkgs/applications/science/biology/kent/default.nix index 2ca5ad191d920..26c55d3dc383a 100644 --- a/pkgs/applications/science/biology/kent/default.nix +++ b/pkgs/applications/science/biology/kent/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , libpng , libuuid , zlib @@ -66,7 +66,7 @@ stdenv.mkDerivation rec { cp $NIX_BUILD_TOP/bin/x86_64/* $out/bin ''; - meta = with stdenv.lib; { + meta = with lib; { description = "UCSC Genome Bioinformatics Group's suite of biological analysis tools, i.e. the kent utilities"; license = licenses.unfree; maintainers = with maintainers; [ scalavision ]; diff --git a/pkgs/applications/science/biology/kssd/default.nix b/pkgs/applications/science/biology/kssd/default.nix index 621a8ce157655..ef853d0cd47c2 100644 --- a/pkgs/applications/science/biology/kssd/default.nix +++ b/pkgs/applications/science/biology/kssd/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, zlib, automake, autoconf, libtool }: +{ lib, stdenv, fetchurl, zlib, automake, autoconf, libtool }: stdenv.mkDerivation rec { pname = "kssd"; @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { install -vD kssd $out/bin/kssd ''; - meta = with stdenv.lib; { + meta = with lib; { description = "K-mer substring space decomposition"; license = licenses.asl20; homepage = "https://github.com/yhg926/public_kssd"; diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 6db7ae55da84a..3a36a2194a134 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, unzip, zlib, python3, parallel }: +{ lib, stdenv, fetchurl, unzip, zlib, python3, parallel }: stdenv.mkDerivation rec { pname = "last"; @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { done ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Genomic sequence aligner"; homepage = "http://last.cbrc.jp/"; license = licenses.gpl3; diff --git a/pkgs/applications/science/biology/lumpy/default.nix b/pkgs/applications/science/biology/lumpy/default.nix index f6267a2e017f8..91a001744474c 100644 --- a/pkgs/applications/science/biology/lumpy/default.nix +++ b/pkgs/applications/science/biology/lumpy/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba +{ lib, stdenv, fetchFromGitHub, htslib, zlib, curl, openssl, samblaster, sambamba , samtools, hexdump, python2Packages, which }: let @@ -39,7 +39,7 @@ in stdenv.mkDerivation rec { sed -i 's|/build/source|'$out'|' $out/bin/lumpyexpress.config ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Probabilistic structural variant caller"; homepage = "https://github.com/arq5x/lumpy-sv"; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/macse/default.nix b/pkgs/applications/science/biology/macse/default.nix index 59938addbe825..c78e142dcc6b9 100644 --- a/pkgs/applications/science/biology/macse/default.nix +++ b/pkgs/applications/science/biology/macse/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, jre, makeWrapper }: +{ lib, stdenv, fetchurl, jre, makeWrapper }: stdenv.mkDerivation rec { pname = "macse"; @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { runHook postInstall ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Multiple alignment of coding sequences"; homepage = "https://bioweb.supagro.inra.fr/macse/"; license = licenses.gpl2; diff --git a/pkgs/applications/science/biology/manta/default.nix b/pkgs/applications/science/biology/manta/default.nix index f0f0575e055a2..1f46e0141da33 100644 --- a/pkgs/applications/science/biology/manta/default.nix +++ b/pkgs/applications/science/biology/manta/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, zlib, python2 }: +{ lib, stdenv, fetchFromGitHub, cmake, zlib, python2 }: stdenv.mkDerivation rec { pname = "manta"; @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { PYTHONPATH=$out/lib/python/pyflow:$PYTHONPATH python -c 'import pyflowTaskWrapper; import pyflow' ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Structural variant caller"; license = licenses.gpl3; homepage = "https://github.com/Illumina/manta"; diff --git a/pkgs/applications/science/biology/megahit/default.nix b/pkgs/applications/science/biology/megahit/default.nix index 3168ecb1cf832..ee2f16f389b25 100644 --- a/pkgs/applications/science/biology/megahit/default.nix +++ b/pkgs/applications/science/biology/megahit/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, zlib }: +{ lib, stdenv, fetchFromGitHub, cmake, zlib }: stdenv.mkDerivation rec { pname = "megahit"; @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; buildInputs = [ zlib ]; - meta = with stdenv.lib; { + meta = with lib; { description = "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph"; license = licenses.gpl3; homepage = "https://github.com/voutcn/megahit"; diff --git a/pkgs/applications/science/biology/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix index 897c1994a5008..3dece25915b47 100644 --- a/pkgs/applications/science/biology/minc-tools/default.nix +++ b/pkgs/applications/science/biology/minc-tools/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, makeWrapper, flex, bison, perl, TextFormat, +{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper, flex, bison, perl, TextFormat, libminc, libjpeg, nifticlib, zlib }: stdenv.mkDerivation rec { @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { done ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/BIC-MNI/minc-tools"; description = "Command-line utilities for working with MINC files"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/pkgs/applications/science/biology/minc-widgets/default.nix b/pkgs/applications/science/biology/minc-widgets/default.nix index 497c39a52a4c2..3af227d70a5a0 100644 --- a/pkgs/applications/science/biology/minc-widgets/default.nix +++ b/pkgs/applications/science/biology/minc-widgets/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, makeWrapper, +{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, libminc, octave, coreutils, minc_tools }: @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { done ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/BIC-MNI/${pname}"; description = "Collection of Perl and shell scripts for processing MINC files"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/pkgs/applications/science/biology/minia/default.nix b/pkgs/applications/science/biology/minia/default.nix index 2a80de733b08f..6b6bc300e0d9f 100644 --- a/pkgs/applications/science/biology/minia/default.nix +++ b/pkgs/applications/science/biology/minia/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, hdf5, boost }: +{ lib, stdenv, fetchFromGitHub, cmake, hdf5, boost }: stdenv.mkDerivation rec { pname = "minia"; @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { rm -rf thirdparty/gatb-core/gatb-core/thirdparty/{hdf5,boost} ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Short read genome assembler"; homepage = "https://github.com/GATB/minia"; license = licenses.agpl3; diff --git a/pkgs/applications/science/biology/minimap2/default.nix b/pkgs/applications/science/biology/minimap2/default.nix index e33a17537910b..ae327e2c43fd7 100644 --- a/pkgs/applications/science/biology/minimap2/default.nix +++ b/pkgs/applications/science/biology/minimap2/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, zlib }: +{ lib, stdenv, fetchFromGitHub, zlib }: stdenv.mkDerivation rec { pname = "minimap2"; @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { cp minimap2.1 $out/share/man/man1 ''; - meta = with stdenv.lib; { + meta = with lib; { description = "A versatile pairwise aligner for genomic and spliced nucleotide sequences"; homepage = "https://lh3.github.io/minimap2"; license = licenses.mit; diff --git a/pkgs/applications/science/biology/mni_autoreg/default.nix b/pkgs/applications/science/biology/mni_autoreg/default.nix index 40ec9e0de6d21..b0ec8a70e149a 100644 --- a/pkgs/applications/science/biology/mni_autoreg/default.nix +++ b/pkgs/applications/science/biology/mni_autoreg/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, libminc }: +{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, libminc }: stdenv.mkDerivation rec { pname = "mni_autoreg"; @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { done ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/BIC-MNI/mni_autoreg"; description = "Tools for automated registration using the MINC image format"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/pkgs/applications/science/biology/mosdepth/default.nix b/pkgs/applications/science/biology/mosdepth/default.nix index d2b05943f7cea..4815ddf2f75c9 100644 --- a/pkgs/applications/science/biology/mosdepth/default.nix +++ b/pkgs/applications/science/biology/mosdepth/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchFromGitHub, nim, htslib, pcre}: +{lib, stdenv, fetchFromGitHub, nim, htslib, pcre}: let hts-nim = fetchFromGitHub { @@ -36,7 +36,7 @@ in stdenv.mkDerivation rec { installPhase = "install -Dt $out/bin mosdepth"; - meta = with stdenv.lib; { + meta = with lib; { description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing"; license = licenses.mit; homepage = "https://github.com/brentp/mosdepth"; diff --git a/pkgs/applications/science/biology/mrbayes/default.nix b/pkgs/applications/science/biology/mrbayes/default.nix index 0ebd144112166..9acfea1a14631 100644 --- a/pkgs/applications/science/biology/mrbayes/default.nix +++ b/pkgs/applications/science/biology/mrbayes/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchurl, readline}: +{lib, stdenv, fetchurl, readline}: stdenv.mkDerivation rec { # FIXME: replace Makefile so we can build MPI & MAC support @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { builder = ./builder.sh; buildInputs = [readline]; - meta = with stdenv.lib; { + meta = with lib; { description = "Bayesian Inference of Phylogeny"; longDescription = '' Bayesian inference of phylogeny is based upon a diff --git a/pkgs/applications/science/biology/muscle/default.nix b/pkgs/applications/science/biology/muscle/default.nix index 7ed18349259e3..e7c1040e59308 100644 --- a/pkgs/applications/science/biology/muscle/default.nix +++ b/pkgs/applications/science/biology/muscle/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl }: +{ lib, stdenv, fetchurl }: stdenv.mkDerivation rec { _name = "muscle"; @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { install -vD muscle $out/bin/muscle ''; - meta = with stdenv.lib; { + meta = with lib; { description = "A multiple sequence alignment method with reduced time and space complexity"; license = licenses.publicDomain; homepage = "https://www.drive5.com/muscle/"; diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix index 8cad5f466c5f0..048a9a5644d0d 100644 --- a/pkgs/applications/science/biology/neuron/default.nix +++ b/pkgs/applications/science/biology/neuron/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchurl , pkgconfig , automake @@ -68,7 +68,7 @@ stdenv.mkDerivation rec { propagatedBuildInputs = [ readline ncurses which libtool ]; - meta = with stdenv.lib; { + meta = with 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 diff --git a/pkgs/applications/science/biology/niftyreg/default.nix b/pkgs/applications/science/biology/niftyreg/default.nix index 4e965d70fe310..d5f625893e925 100644 --- a/pkgs/applications/science/biology/niftyreg/default.nix +++ b/pkgs/applications/science/biology/niftyreg/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, cmake, zlib }: +{ lib, stdenv, fetchurl, cmake, zlib }: stdenv.mkDerivation rec { pname = "niftyreg"; @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; buildInputs = [ zlib ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg"; description = "Medical image registration software"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/pkgs/applications/science/biology/niftyseg/default.nix b/pkgs/applications/science/biology/niftyseg/default.nix index 98cca7815eaa7..215ee35d78a47 100644 --- a/pkgs/applications/science/biology/niftyseg/default.nix +++ b/pkgs/applications/science/biology/niftyseg/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, cmake, eigen, zlib }: +{ lib, stdenv, fetchurl, cmake, eigen, zlib }: stdenv.mkDerivation rec { pname = "niftyseg"; @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ cmake ]; buildInputs = [ eigen zlib ]; - meta = with stdenv.lib; { + meta = with 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 ]; diff --git a/pkgs/applications/science/biology/octopus/default.nix b/pkgs/applications/science/biology/octopus/default.nix index 7dee07275a0f0..b7a4a4c1a2a0a 100644 --- a/pkgs/applications/science/biology/octopus/default.nix +++ b/pkgs/applications/science/biology/octopus/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, lzma, pkg-config}: +{lib, stdenv, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, lzma, pkg-config}: stdenv.mkDerivation rec { pname = "octopus"; @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { mv $out/octopus $out/bin ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Bayesian haplotype-based mutation calling"; license = licenses.mit; homepage = "https://github.com/luntergroup/octopus"; diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index af29dd77ac28d..d18ca2e2a4f8b 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchurl, jre, makeWrapper}: +{lib, stdenv, fetchurl, jre, makeWrapper}: stdenv.mkDerivation rec { pname = "picard-tools"; @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { makeWrapper ${jre}/bin/java $out/bin/picard --add-flags "-jar $out/libexec/picard/picard.jar" ''; - meta = with stdenv.lib; { + meta = with 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/"; diff --git a/pkgs/applications/science/biology/platypus/default.nix b/pkgs/applications/science/biology/platypus/default.nix index 30e45d5af0ecb..30bc68fb0e874 100644 --- a/pkgs/applications/science/biology/platypus/default.nix +++ b/pkgs/applications/science/biology/platypus/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchFromGitHub, python27, htslib, zlib, makeWrapper}: +{lib, stdenv, fetchFromGitHub, python27, htslib, zlib, makeWrapper}: let python = python27.withPackages (ps: with ps; [ cython ]); @@ -28,7 +28,7 @@ in stdenv.mkDerivation { makeWrapper ${python}/bin/python $out/bin/platypus --add-flags "$out/libexec/platypus/bin/Platypus.py" ''; - meta = with stdenv.lib; { + meta = with lib; { description = "The Platypus variant caller"; license = licenses.gpl3; homepage = "https://github.com/andyrimmer/Platypus"; diff --git a/pkgs/applications/science/biology/prodigal/default.nix b/pkgs/applications/science/biology/prodigal/default.nix index ba51c93c38c25..70069fe541d19 100644 --- a/pkgs/applications/science/biology/prodigal/default.nix +++ b/pkgs/applications/science/biology/prodigal/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub }: +{ lib, stdenv, fetchFromGitHub }: stdenv.mkDerivation rec { pname = "prodigal"; @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { "INSTALLDIR=$(out)/bin" ]; - meta = with stdenv.lib; { + meta = with lib; { description = "Fast, reliable protein-coding gene prediction for prokaryotic genomes"; homepage = "https://github.com/hyattpd/Prodigal"; license = licenses.gpl3; diff --git a/pkgs/applications/science/biology/raxml/default.nix b/pkgs/applications/science/biology/raxml/default.nix index a77505c1b3f81..e4019295ece14 100644 --- a/pkgs/applications/science/biology/raxml/default.nix +++ b/pkgs/applications/science/biology/raxml/default.nix @@ -1,4 +1,4 @@ -{ stdenv +{ lib, stdenv , fetchFromGitHub , pkgs , mpi ? false @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { mkdir -p $out/bin && cp raxmlHPC-PTHREADS-SSE3 $out/bin ''; - meta = with stdenv.lib; { + meta = with lib; { description = "A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies"; license = licenses.gpl3; homepage = "https://sco.h-its.org/exelixis/web/software/raxml/"; diff --git a/pkgs/applications/science/biology/sambamba/default.nix b/pkgs/applications/science/biology/sambamba/default.nix index 7e33a66121890..8802736efac81 100644 --- a/pkgs/applications/science/biology/sambamba/default.nix +++ b/pkgs/applications/science/biology/sambamba/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, python3, which, dmd, ldc, zlib }: +{ lib, stdenv, fetchFromGitHub, python3, which, dmd, ldc, zlib }: stdenv.mkDerivation rec { pname = "sambamba"; @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { cp bin/sambamba-${version} $out/bin/sambamba ''; - meta = with stdenv.lib; { + meta = with lib; { description = "SAM/BAM processing tool"; homepage = "https://lomereiter.github.io/sambamba/"; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/samblaster/default.nix b/pkgs/applications/science/biology/samblaster/default.nix index 6846e3c84fae4..48c19666ba046 100644 --- a/pkgs/applications/science/biology/samblaster/default.nix +++ b/pkgs/applications/science/biology/samblaster/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub }: +{ lib, stdenv, fetchFromGitHub }: stdenv.mkDerivation rec { pname = "samblaster"; @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { cp samblaster $out/bin ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Tool for marking duplicates and extracting discordant/split reads from SAM/BAM files"; maintainers = with maintainers; [ jbedo ]; license = licenses.mit; diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix index 27ed79a1f6ca5..7dd78ee2e635c 100644 --- a/pkgs/applications/science/biology/samtools/default.nix +++ b/pkgs/applications/science/biology/samtools/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, zlib, htslib, perl, ncurses ? null }: +{ lib, stdenv, fetchurl, zlib, htslib, perl, ncurses ? null }: stdenv.mkDerivation rec { pname = "samtools"; @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { doCheck = true; - meta = with stdenv.lib; { + meta = with lib; { description = "Tools for manipulating SAM/BAM/CRAM format"; license = licenses.mit; homepage = "http://www.htslib.org/"; diff --git a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix index d62c2a1fe7b1a..590f10dd87a1a 100644 --- a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix +++ b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, zlib }: +{ lib, stdenv, fetchurl, zlib }: stdenv.mkDerivation rec { pname = "samtools"; @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { cp samtools.1 $out/share/man ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Tools for manipulating SAM/BAM/CRAM format"; license = licenses.mit; homepage = "http://samtools.sourceforge.net/"; diff --git a/pkgs/applications/science/biology/seaview/default.nix b/pkgs/applications/science/biology/seaview/default.nix index dfee979478251..27d83f3bf89ed 100644 --- a/pkgs/applications/science/biology/seaview/default.nix +++ b/pkgs/applications/science/biology/seaview/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, coreutils, fltk, libjpeg }: +{ lib, stdenv, fetchurl, coreutils, fltk, libjpeg }: stdenv.mkDerivation rec { version = "5.0.4"; @@ -14,7 +14,7 @@ stdenv.mkDerivation rec { patchPhase = "sed -i 's#PATH=/bin:/usr/bin rm#'${coreutils}/bin/rm'#' seaview.cxx"; installPhase = "mkdir -p $out/bin; cp seaview $out/bin"; - meta = with stdenv.lib; { + meta = with lib; { description = "GUI for molecular phylogeny"; longDescription = '' SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. diff --git a/pkgs/applications/science/biology/snpeff/default.nix b/pkgs/applications/science/biology/snpeff/default.nix index 941f107a580fe..32701af8392cc 100644 --- a/pkgs/applications/science/biology/snpeff/default.nix +++ b/pkgs/applications/science/biology/snpeff/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchurl, jre, unzip, makeWrapper}: +{lib, stdenv, fetchurl, jre, unzip, makeWrapper}: stdenv.mkDerivation rec { pname = "snpeff"; @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { makeWrapper ${jre}/bin/java $out/bin/snpsift --add-flags "-jar $out/libexec/snpeff/SnpSift.jar" ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Genetic variant annotation and effect prediction toolbox"; license = licenses.lgpl3; homepage = "http://snpeff.sourceforge.net/"; diff --git a/pkgs/applications/science/biology/somatic-sniper/default.nix b/pkgs/applications/science/biology/somatic-sniper/default.nix index 298bb98ec990c..034409cfb013d 100644 --- a/pkgs/applications/science/biology/somatic-sniper/default.nix +++ b/pkgs/applications/science/biology/somatic-sniper/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchFromGitHub, cmake, zlib, ncurses}: +{lib, stdenv, fetchFromGitHub, cmake, zlib, ncurses}: stdenv.mkDerivation rec { pname = "somatic-sniper"; @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { enableParallelBuilding = false; - meta = with stdenv.lib; { + meta = with lib; { description = "Identify single nucleotide positions that are different between tumor and normal"; license = licenses.mit; homepage = "https://github.com/genome/somatic-sniper"; diff --git a/pkgs/applications/science/biology/sortmerna/default.nix b/pkgs/applications/science/biology/sortmerna/default.nix index 4e32669dfca92..01c65f4bcff48 100644 --- a/pkgs/applications/science/biology/sortmerna/default.nix +++ b/pkgs/applications/science/biology/sortmerna/default.nix @@ -1,4 +1,4 @@ -{ stdenv, cmake, rocksdb, rapidjson, pkgconfig, fetchFromGitHub, fetchpatch, zlib }: +{ lib, stdenv, cmake, rocksdb, rapidjson, pkgconfig, fetchFromGitHub, fetchpatch, zlib }: stdenv.mkDerivation rec { pname = "sortmerna"; @@ -35,7 +35,7 @@ stdenv.mkDerivation rec { "target_link_libraries(sortmerna Threads::Threads" ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data"; license = licenses.lgpl3; platforms = platforms.x86_64; diff --git a/pkgs/applications/science/biology/spades/default.nix b/pkgs/applications/science/biology/spades/default.nix index 776719579d979..ec381693aedfb 100644 --- a/pkgs/applications/science/biology/spades/default.nix +++ b/pkgs/applications/science/biology/spades/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, zlib, bzip2, cmake, python3 }: +{ lib, stdenv, fetchurl, zlib, bzip2, cmake, python3 }: stdenv.mkDerivation rec { pname = "SPAdes"; @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { sourceRoot = "${pname}-${version}/src"; - meta = with stdenv.lib; { + meta = with lib; { description = "St. Petersburg genome assembler: assembly toolkit containing various assembly pipelines"; license = licenses.gpl2; homepage = "http://cab.spbu.ru/software/spades/"; diff --git a/pkgs/applications/science/biology/star/default.nix b/pkgs/applications/science/biology/star/default.nix index f2e1a2a8fee55..a7fe948ecfd60 100644 --- a/pkgs/applications/science/biology/star/default.nix +++ b/pkgs/applications/science/biology/star/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, zlib }: +{ lib, stdenv, fetchFromGitHub, zlib }: stdenv.mkDerivation rec { pname = "star"; @@ -29,7 +29,7 @@ stdenv.mkDerivation rec { runHook postInstall ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Spliced Transcripts Alignment to a Reference"; homepage = "https://github.com/alexdobin/STAR"; license = licenses.gpl3Plus; diff --git a/pkgs/applications/science/biology/strelka/default.nix b/pkgs/applications/science/biology/strelka/default.nix index a32eddcb1cd93..8585f3770fbcd 100644 --- a/pkgs/applications/science/biology/strelka/default.nix +++ b/pkgs/applications/science/biology/strelka/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchFromGitHub, cmake, zlib, python2}: +{lib, stdenv, fetchFromGitHub, cmake, zlib, python2}: stdenv.mkDerivation rec { pname = "strelka"; @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { popd ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Germline and small variant caller"; license = licenses.gpl3; homepage = "https://github.com/Illumina/strelka"; diff --git a/pkgs/applications/science/biology/sumatools/default.nix b/pkgs/applications/science/biology/sumatools/default.nix index 1e3b479d54fc7..2a30f33172b95 100644 --- a/pkgs/applications/science/biology/sumatools/default.nix +++ b/pkgs/applications/science/biology/sumatools/default.nix @@ -1,8 +1,8 @@ -{ gccStdenv, fetchFromGitLab, zlib }: +{ lib, gccStdenv, fetchFromGitLab, zlib }: let stdenv = gccStdenv; - meta = with stdenv.lib; { + meta = with lib; { description = "Fast and exact comparison and clustering of sequences"; homepage = "https://metabarcoding.org/sumatra"; maintainers = [ maintainers.bzizou ]; diff --git a/pkgs/applications/science/biology/svaba/default.nix b/pkgs/applications/science/biology/svaba/default.nix index ae8dc95d6fea2..87b77f6ac0456 100644 --- a/pkgs/applications/science/biology/svaba/default.nix +++ b/pkgs/applications/science/biology/svaba/default.nix @@ -1,4 +1,4 @@ -{ stdenv, zlib, bzip2, lzma, fetchFromGitHub } : +{ lib, stdenv, zlib, bzip2, lzma, fetchFromGitHub } : stdenv.mkDerivation rec { version = "1.1.0"; @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { runHook postInstall ''; - meta = with stdenv.lib; { + meta = with 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"; diff --git a/pkgs/applications/science/biology/tebreak/default.nix b/pkgs/applications/science/biology/tebreak/default.nix index 82c624ba7cd9e..b70ac29e38f79 100644 --- a/pkgs/applications/science/biology/tebreak/default.nix +++ b/pkgs/applications/science/biology/tebreak/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa +{ lib, stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa , samtools, findutils, python }: python3Packages.buildPythonApplication rec { @@ -38,7 +38,7 @@ python3Packages.buildPythonApplication rec { ${python.interpreter} checktest.py ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Find and characterise transposable element insertions"; homepage = "https://github.com/adamewing/tebreak"; license = licenses.mit; diff --git a/pkgs/applications/science/biology/trimal/default.nix b/pkgs/applications/science/biology/trimal/default.nix index 8d7e62b614316..b27a63a2135ae 100755 --- a/pkgs/applications/science/biology/trimal/default.nix +++ b/pkgs/applications/science/biology/trimal/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub }: +{ lib, stdenv, fetchFromGitHub }: stdenv.mkDerivation rec { pname = "trimal"; @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { cp -a trimal readal statal $out/bin ''; - meta = with stdenv.lib; { + meta = with lib; { description = "A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment"; license = licenses.gpl3; platforms = platforms.linux; diff --git a/pkgs/applications/science/biology/varscan/default.nix b/pkgs/applications/science/biology/varscan/default.nix index 2c395650e175d..65a19b83a70ec 100644 --- a/pkgs/applications/science/biology/varscan/default.nix +++ b/pkgs/applications/science/biology/varscan/default.nix @@ -1,4 +1,4 @@ -{stdenv, fetchurl, jre, makeWrapper}: +{lib, stdenv, fetchurl, jre, makeWrapper}: stdenv.mkDerivation rec { pname = "varscan"; @@ -20,7 +20,7 @@ stdenv.mkDerivation rec { makeWrapper ${jre}/bin/java $out/bin/varscan --add-flags "-jar $out/libexec/varscan/varscan.jar" ''; - meta = with stdenv.lib; { + meta = with 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 diff --git a/pkgs/applications/science/biology/vcftools/default.nix b/pkgs/applications/science/biology/vcftools/default.nix index 52957b58bc929..61b2ea143b8d5 100755 --- a/pkgs/applications/science/biology/vcftools/default.nix +++ b/pkgs/applications/science/biology/vcftools/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, zlib, autoreconfHook, pkgconfig, perl }: +{ lib, stdenv, fetchFromGitHub, zlib, autoreconfHook, pkgconfig, perl }: stdenv.mkDerivation rec { pname = "vcftools"; @@ -13,7 +13,7 @@ stdenv.mkDerivation rec { buildInputs = [ autoreconfHook pkgconfig zlib perl ]; - meta = with stdenv.lib; { + meta = with 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; diff --git a/pkgs/applications/science/biology/whisper/default.nix b/pkgs/applications/science/biology/whisper/default.nix index 9e336600202b3..8552eede170bc 100644 --- a/pkgs/applications/science/biology/whisper/default.nix +++ b/pkgs/applications/science/biology/whisper/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, fetchurl }: +{ lib, stdenv, fetchFromGitHub, fetchurl }: stdenv.mkDerivation rec { pname = "whisper"; @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { runHook postInstall ''; - meta = with stdenv.lib; { + meta = with lib; { description = "Short read sequence mapper"; license = licenses.gpl3; homepage = "https://github.com/refresh-bio/whisper"; |