diff --git a/pkgs/fastqc.nix b/pkgs/fastqc.nix index dd1d5c2..43d8272 100644 --- a/pkgs/fastqc.nix +++ b/pkgs/fastqc.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub +{ stdenv, lib, fetchFromGitHub , jdk, ant, makeWrapper , jre, perl }: diff --git a/pkgs/firedrake/exodus.nix b/pkgs/firedrake/exodus.nix index e9ef408..12ef90a 100644 --- a/pkgs/firedrake/exodus.nix +++ b/pkgs/firedrake/exodus.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, cmake, gfortran +{ stdenv, lib, fetchurl, cmake, gfortran , netcdf, hdf5 }: stdenv.mkDerivation rec { diff --git a/pkgs/firedrake/hypre.nix b/pkgs/firedrake/hypre.nix index 9c593f7..0bf1199 100644 --- a/pkgs/firedrake/hypre.nix +++ b/pkgs/firedrake/hypre.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, cmake +{ stdenv, lib, fetchFromGitHub, cmake , openmpi }: stdenv.mkDerivation rec { diff --git a/pkgs/firedrake/metis.nix b/pkgs/firedrake/metis.nix index a10e115..a829e56 100644 --- a/pkgs/firedrake/metis.nix +++ b/pkgs/firedrake/metis.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromBitbucket, cmake }: +{ stdenv, lib, fetchFromBitbucket, cmake }: stdenv.mkDerivation rec { version = "5.1.0-p4"; diff --git a/pkgs/firedrake/parmetis.nix b/pkgs/firedrake/parmetis.nix index 4dcdf38..e21a76b 100644 --- a/pkgs/firedrake/parmetis.nix +++ b/pkgs/firedrake/parmetis.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromBitbucket, cmake +{ stdenv, lib, fetchFromBitbucket, cmake , openmpi , metis }: diff --git a/pkgs/firedrake/petsc.nix b/pkgs/firedrake/petsc.nix index 9c35088..4bba98d 100644 --- a/pkgs/firedrake/petsc.nix +++ b/pkgs/firedrake/petsc.nix @@ -1,4 +1,4 @@ -{ stdenv, callPackage, writeText, fetchFromGitHub, python, gfortran +{ stdenv, lib, callPackage, writeText, fetchFromGitHub, python, gfortran , openmpi, blas, liblapack, hdf5, netcdf, eigen , sowing, metis, hypre, parmetis, exodus }: diff --git a/pkgs/firedrake/sowing.nix b/pkgs/firedrake/sowing.nix index 3521eb7..1580e43 100644 --- a/pkgs/firedrake/sowing.nix +++ b/pkgs/firedrake/sowing.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromBitbucket, ghostscript }: +{ stdenv, lib, fetchFromBitbucket, ghostscript }: stdenv.mkDerivation rec { version = "1.1.25-p1"; diff --git a/pkgs/ghmm/default.nix b/pkgs/ghmm/default.nix index 15c35de..0523319 100644 --- a/pkgs/ghmm/default.nix +++ b/pkgs/ghmm/default.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchsvn, autoreconfHook, pkg-config +{ stdenv, lib, fetchsvn, autoreconfHook, pkg-config , libxml2, python2Packages, swig }: stdenv.mkDerivation rec { diff --git a/pkgs/gsort/default.nix b/pkgs/gsort/default.nix index 33c62ad..8418f52 100644 --- a/pkgs/gsort/default.nix +++ b/pkgs/gsort/default.nix @@ -1,5 +1,5 @@ # This file was generated by https://github.com/kamilchm/go2nix v1.3.0 -{ stdenv, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn }: +{ stdenv, lib, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn }: buildGoPackage rec { name = "gsort-${version}"; diff --git a/pkgs/idba.nix b/pkgs/idba.nix index 1a62888..46990a5 100644 --- a/pkgs/idba.nix +++ b/pkgs/idba.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl +{ stdenv, lib, fetchurl , bash }: stdenv.mkDerivation rec { diff --git a/pkgs/lumpy.nix b/pkgs/lumpy.nix index 1f27bf2..e8da265 100644 --- a/pkgs/lumpy.nix +++ b/pkgs/lumpy.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, which, autoconf, automake +{ stdenv, lib, fetchFromGitHub, which, autoconf, automake , zlib, curl , python2, hexdump, sambamba, samblaster, samtools }: diff --git a/pkgs/meraculous.nix b/pkgs/meraculous.nix index 104c9bc..cef204e 100644 --- a/pkgs/meraculous.nix +++ b/pkgs/meraculous.nix @@ -1,4 +1,4 @@ -{ stdenv, overrideCC, gcc49, fetchurl, makeWrapper, gzip, cmake +{ stdenv, lib, overrideCC, gcc49, fetchurl, makeWrapper, gzip, cmake , boost, perl, perlPackages, gnuplot }: # gcc 5.x c++11 requires istream to be explicitly cast to bool diff --git a/pkgs/mfix/mfixsolver.nix b/pkgs/mfix/mfixsolver.nix index 1439c6d..d616379 100644 --- a/pkgs/mfix/mfixsolver.nix +++ b/pkgs/mfix/mfixsolver.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, fetchFromGitHub +{ stdenv, lib, fetchurl, fetchFromGitHub , cmake, gfortran, python38, pkg-config , openmpi, netcdf, boost }: diff --git a/pkgs/openfoam.nix b/pkgs/openfoam.nix index 391b89e..cb4c2ed 100644 --- a/pkgs/openfoam.nix +++ b/pkgs/openfoam.nix @@ -1,4 +1,4 @@ -{ stdenv, bashInteractive, fetchFromGitHub, makeWrapper, flex, bison +{ stdenv, lib, bashInteractive, fetchFromGitHub, makeWrapper, flex, bison , zlib, boost, openmpi, readline, gperftools, cgal, metis, scotch, mpfr }: diff --git a/pkgs/openslide/default.nix b/pkgs/openslide/default.nix index 290cb79..897f1fa 100644 --- a/pkgs/openslide/default.nix +++ b/pkgs/openslide/default.nix @@ -1,4 +1,4 @@ -{ stdenv, autoreconfHook, pkg-config, fetchFromGitHub +{ stdenv, lib, autoreconfHook, pkg-config, fetchFromGitHub , zlib, openjpeg, libtiff, cairo, libpng, gdk-pixbuf, libxml2, sqlite }: stdenv.mkDerivation rec { diff --git a/pkgs/sambamba.nix b/pkgs/sambamba.nix index 3e71cb7..2e5ada5 100644 --- a/pkgs/sambamba.nix +++ b/pkgs/sambamba.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub, ldc +{ stdenv, lib, fetchFromGitHub, ldc , python3, glibc, which, zlib }: stdenv.mkDerivation rec { diff --git a/pkgs/samblaster.nix b/pkgs/samblaster.nix index e73f27e..0a3770c 100644 --- a/pkgs/samblaster.nix +++ b/pkgs/samblaster.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchFromGitHub }: +{ stdenv, lib, fetchFromGitHub }: stdenv.mkDerivation rec { version = "0.1.24"; diff --git a/pkgs/smoove/default.nix b/pkgs/smoove/default.nix index d215591..5dd0c99 100644 --- a/pkgs/smoove/default.nix +++ b/pkgs/smoove/default.nix @@ -1,5 +1,5 @@ # This file was generated by https://github.com/kamilchm/go2nix v1.3.0 -{ stdenv, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn, makeWrapper +{ stdenv, lib, buildGoPackage, fetchgit, fetchhg, fetchbzr, fetchsvn, makeWrapper , gzip, gsort, htslib, lumpy, samtools, svtyper, mosdepth }: buildGoPackage rec { diff --git a/pkgs/sumo.nix b/pkgs/sumo.nix index a467b84..c8f90f1 100644 --- a/pkgs/sumo.nix +++ b/pkgs/sumo.nix @@ -1,4 +1,4 @@ -{ stdenv, fetchurl, unzip +{ stdenv, lib, fetchurl, unzip , lzma, bzip2, zlib, libjpeg, libtiff, openssl , mesa, xorg , fox, xercesc, proj, gdal, hdf5, curl }: