From 016a641c38712a6e0e4a94d2c8152958f4db682f Mon Sep 17 00:00:00 2001 From: David Crompton Date: Tue, 23 May 2023 14:24:16 -0400 Subject: [PATCH] stdenv.lib -> lib --- pkgs/fastqc.nix | 2 +- pkgs/firedrake/exodus.nix | 2 +- pkgs/firedrake/hypre.nix | 2 +- pkgs/firedrake/metis.nix | 2 +- pkgs/firedrake/parmetis.nix | 2 +- pkgs/firedrake/petsc.nix | 2 +- pkgs/firedrake/sowing.nix | 2 +- pkgs/ghmm/default.nix | 2 +- pkgs/gsort/default.nix | 2 +- pkgs/idba.nix | 2 +- pkgs/lumpy.nix | 2 +- pkgs/meraculous.nix | 2 +- pkgs/mfix/mfixsolver.nix | 2 +- pkgs/openfoam.nix | 2 +- pkgs/openslide/default.nix | 2 +- pkgs/sambamba.nix | 2 +- pkgs/samblaster.nix | 2 +- pkgs/smoove/default.nix | 2 +- pkgs/sumo.nix | 2 +- 19 files changed, 19 insertions(+), 19 deletions(-) diff --git a/pkgs/fastqc.nix b/pkgs/fastqc.nix index 26451a2..dd1d5c2 100644 --- a/pkgs/fastqc.nix +++ b/pkgs/fastqc.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { makeWrapper $out/share/FastQC/fastqc $out/bin/fastqc --add-flags --java=${jre}/bin/java ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = https://www.bioinformatics.babraham.ac.uk/projects/fastqc/; description = "A quality control tool for high throughput sequence data"; longDescription = '' diff --git a/pkgs/firedrake/exodus.nix b/pkgs/firedrake/exodus.nix index d8f7a11..e9ef408 100644 --- a/pkgs/firedrake/exodus.nix +++ b/pkgs/firedrake/exodus.nix @@ -21,7 +21,7 @@ stdenv.mkDerivation rec { patches = ./exodus-include.patch; sourceRoot = "${name}/exodus"; - meta = with stdenv.lib; { + meta = with lib; { homepage = "http://gsjaardema.github.io/seacas"; description = "A model developed to store and retrieve data for finite element analyses."; license = licenses.bsd3; diff --git a/pkgs/firedrake/hypre.nix b/pkgs/firedrake/hypre.nix index 8f47979..9c593f7 100644 --- a/pkgs/firedrake/hypre.nix +++ b/pkgs/firedrake/hypre.nix @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { makeFlags = [ "VERBOSE=1" ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "http://www.llnl.gov/casc/hypre"; description = "Parallel solvers for sparse linear systems featuring multigrid methods."; license = licenses.gpl2; diff --git a/pkgs/firedrake/metis.nix b/pkgs/firedrake/metis.nix index c94568f..a10e115 100644 --- a/pkgs/firedrake/metis.nix +++ b/pkgs/firedrake/metis.nix @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { makeFlags = [ "VERBOSE=1" ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://bitbucket.org/petsc/metis"; description = "A set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices."; }; diff --git a/pkgs/firedrake/parmetis.nix b/pkgs/firedrake/parmetis.nix index 6df36c1..4dcdf38 100644 --- a/pkgs/firedrake/parmetis.nix +++ b/pkgs/firedrake/parmetis.nix @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { cmakeFlags = [ "-DGKLIB_PATH=../headers" ]; makeFlags = [ "VERBOSE=1" ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "http://glaros.dtc.umn.edu/gkhome/metis/parmetis"; description = "An MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices."; }; diff --git a/pkgs/firedrake/petsc.nix b/pkgs/firedrake/petsc.nix index 96e1789..9c35088 100644 --- a/pkgs/firedrake/petsc.nix +++ b/pkgs/firedrake/petsc.nix @@ -45,7 +45,7 @@ stdenv.mkDerivation rec { setupHook = writeText "setupHook.sh" "export PETSC_DIR=@out@"; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://github.com/firedrakeproject/petsc"; description = "A suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations."; license = licenses.bsd2; diff --git a/pkgs/firedrake/sowing.nix b/pkgs/firedrake/sowing.nix index b8da774..3521eb7 100644 --- a/pkgs/firedrake/sowing.nix +++ b/pkgs/firedrake/sowing.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { ghostscript ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = "https://bitbucket.org/petsc/pkg-sowing"; description = "Tools that are part of the petsc program development and maintenance environment."; }; diff --git a/pkgs/ghmm/default.nix b/pkgs/ghmm/default.nix index b5981e6..15c35de 100644 --- a/pkgs/ghmm/default.nix +++ b/pkgs/ghmm/default.nix @@ -45,7 +45,7 @@ stdenv.mkDerivation rec { hardeningDisable = [ "format" ]; - meta = with stdenv.lib; { + meta = with lib; { description = "The General Hidden Markov Model library (GHMM) is a freely available C library implementing efficient data structures and algorithms for basic and extended HMMs with discrete and continous emissions."; homepage = http://ghmm.sourceforge.net; platforms = platforms.all; diff --git a/pkgs/gsort/default.nix b/pkgs/gsort/default.nix index 1c53846..33c62ad 100644 --- a/pkgs/gsort/default.nix +++ b/pkgs/gsort/default.nix @@ -15,7 +15,7 @@ buildGoPackage rec { goDeps = ./deps.nix; - meta = with stdenv.lib; { + meta = with lib; { homepage = https://github.com/brentp/gsort; description = "A tool to sort genomic files according to a genomefile."; platforms = platforms.all; diff --git a/pkgs/idba.nix b/pkgs/idba.nix index f49f42e..1a62888 100644 --- a/pkgs/idba.nix +++ b/pkgs/idba.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { # stdenv # ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = https://github.com/loneknightpy/idba/; description = "Basic iterative de Bruijn graph assembler for second-generation sequencing reads"; longDescription = "IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. IDBA-UD, an extension of IDBA, is designed to utilize paired-end reads to assemble low-depth regions and use progressive depth on contigs to reduce errors in high-depth regions. It is a generic purpose assembler and especially good for single-cell and metagenomic sequencing data. IDBA-Hybrid is another update version of IDBA-UD, which can make use of a similar reference genome to improve assembly result. IDBA-Tran is an iterative de Bruijn graph assembler for RNA-Seq data."; diff --git a/pkgs/lumpy.nix b/pkgs/lumpy.nix index 208065c..1f27bf2 100644 --- a/pkgs/lumpy.nix +++ b/pkgs/lumpy.nix @@ -46,7 +46,7 @@ stdenv.mkDerivation rec { samtools ]; - meta = with stdenv.lib; { + meta = with lib; { description = "A probabilistic framework for structural variant discovery."; homepage = https://github.com/arq5x/lumpy-sv; platforms = platforms.all; diff --git a/pkgs/meraculous.nix b/pkgs/meraculous.nix index 5090269..104c9bc 100644 --- a/pkgs/meraculous.nix +++ b/pkgs/meraculous.nix @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { gnuplot ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = http://jgi.doe.gov/data-and-tools/meraculous; description = "Meraculous is a whole genome assembler for Next Generation Sequencing data geared for large genomes."; platforms = platforms.all; diff --git a/pkgs/mfix/mfixsolver.nix b/pkgs/mfix/mfixsolver.nix index 52c2769..1439c6d 100644 --- a/pkgs/mfix/mfixsolver.nix +++ b/pkgs/mfix/mfixsolver.nix @@ -67,7 +67,7 @@ stdenv.mkDerivation rec { # netcdf ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = https://mfix.netl.doe.gov; description = "An open-source multiphase flow solver"; platforms = platforms.all; diff --git a/pkgs/openfoam.nix b/pkgs/openfoam.nix index a9a352d..391b89e 100644 --- a/pkgs/openfoam.nix +++ b/pkgs/openfoam.nix @@ -84,7 +84,7 @@ stdenv.mkDerivation rec { mpfr ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = http://www.openfoam.com; description = "Free open-source CFD software"; platforms = platforms.linux; diff --git a/pkgs/openslide/default.nix b/pkgs/openslide/default.nix index 592bb15..290cb79 100644 --- a/pkgs/openslide/default.nix +++ b/pkgs/openslide/default.nix @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { sed -i -e 's|AM_CONDITIONAL(\[WINDOWS_RESOURCES\], \[test x$RC != x\])|AM_CONDITIONAL([WINDOWS_RESOURCES], [false])|' configure.ac ''; - meta = with stdenv.lib; { + meta = with lib; { homepage = http://openslide.org; description = "A C library that provides a simple interface to read whole-slide images."; platforms = platforms.all; diff --git a/pkgs/sambamba.nix b/pkgs/sambamba.nix index 55bcb40..3e71cb7 100644 --- a/pkgs/sambamba.nix +++ b/pkgs/sambamba.nix @@ -27,7 +27,7 @@ stdenv.mkDerivation rec { zlib ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = https://github.com/lomereiter/sambamba/wiki; description = "Sambamba is a set of command-line tools for working with SAM/BAM file formats which are used for storing next generation sequencing (NGS) datasets."; platforms = platforms.all; diff --git a/pkgs/samblaster.nix b/pkgs/samblaster.nix index 849f6e7..e73f27e 100644 --- a/pkgs/samblaster.nix +++ b/pkgs/samblaster.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { buildInputs = [ ]; - meta = with stdenv.lib; { + meta = with lib; { description = "A fast and flexible program for marking duplicates in read-id grouped paired-end SAM files."; homepage = https://github.com/GregoryFaust/samblaster; platforms = platforms.all; diff --git a/pkgs/smoove/default.nix b/pkgs/smoove/default.nix index d3e7800..d215591 100644 --- a/pkgs/smoove/default.nix +++ b/pkgs/smoove/default.nix @@ -31,7 +31,7 @@ buildGoPackage rec { makeWrapper ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = https://github.com/brentp/smoove; description = "Wrap existing software and adds some internal read-filtering to simplify calling and genotyping structural variants."; platforms = platforms.all; diff --git a/pkgs/sumo.nix b/pkgs/sumo.nix index d3a4c8b..a467b84 100644 --- a/pkgs/sumo.nix +++ b/pkgs/sumo.nix @@ -24,7 +24,7 @@ stdenv.mkDerivation rec { curl ]; - meta = with stdenv.lib; { + meta = with lib; { homepage = http://software.dlr.de/p/sumo/home; description = "SUMO is an open source, highly portable, microscopic and continuous road traffic simulation package designed to handle large road networks"; platforms = platforms.all;