From cdda264a5a21e3c39bc4d4a5483794f41cd0d54b Mon Sep 17 00:00:00 2001 From: Bruno Vieira Date: Mon, 7 Jan 2019 22:32:56 +0000 Subject: [PATCH] Fix stackoverflow issue with wich custom nix-channel and disable packages for revision --- default.nix | 11 +++-- nixsrc.json | 9 +--- pkgs/top-level/all-packages.nix | 84 ++++++++++++++++----------------- 3 files changed, 49 insertions(+), 55 deletions(-) diff --git a/default.nix b/default.nix index 70469b9..97c9df4 100644 --- a/default.nix +++ b/default.nix @@ -1,7 +1,8 @@ -{ system ? builtins.currentSystem, pkg ? null, timestamp ? "1970-01-01T00:00:01Z" }: +{ system ? builtins.currentSystem }: let - nixpkgs = import { inherit system; }; - makeOverridable = nixpkgs.stdenv.lib.makeOverridable; - pkgs = import ./pkgs/top-level/all-packages.nix; + # nixpkgs = import { inherit system; }; + # makeOverridable = nixpkgs.stdenv.lib.makeOverridable; + pkgs = import ./pkgs/top-level/all-packages.nix { inherit system; }; in - makeOverridable pkgs { inherit system; inherit timestamp; pkg = pkg; shellDir = ./shell.nix; } + # makeOverridable pkgs { inherit system; inherit timestamp; pkg = pkg; shellDir = ./shell.nix; } + pkgs diff --git a/nixsrc.json b/nixsrc.json index d527b5b..8a1a2ba 100644 --- a/nixsrc.json +++ b/nixsrc.json @@ -1,9 +1,4 @@ { - "version": "17.09", - "origin": { - "owner": "NixOS", - "repo": "nixpkgs", - "rev": "39cd40f7bea40116ecb756d46a687bfd0d2e550e", - "sha256": "0kpx4h9p1lhjbn1gsil111swa62hmjs9g93xmsavfiki910s73sh" - } + "version": "18.09", + "sha256": "1ib96has10v5nr6bzf7v8kw7yzww8zanxgw2qi1ll1sbv6kj6zpd" } \ No newline at end of file diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 78df034..37695ec 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -1,12 +1,9 @@ -# Install packages with `nix-env -f default.nix -iA package-name` -{ system ? builtins.currentSystem, pkg ? null, shellDir ? ../../shell.nix, hiPrio ? null, nodejs-6_x ? null, timestamp ? "1970-01-01T00:00:01Z" }: +{ system ? builtins.currentSystem }: let - nixVersion = "18.09"; - pinPkgs = import (builtins.fetchTarball { - name = "nixos-${nixVersion}"; - url = "https://github.com/NixOS/nixpkgs/archive/${nixVersion}.tar.gz"; + name = "nixos-18.09"; + url = "https://github.com/NixOS/nixpkgs/archive/18.09.tar.gz"; sha256 = "1ib96has10v5nr6bzf7v8kw7yzww8zanxgw2qi1ll1sbv6kj6zpd"; }) { inherit system; }; @@ -21,17 +18,17 @@ let callPackage = pkgs.lib.callPackageWith (pkgs // pkgs.xlibs // self); customPkgs = { + nextflow = callPackage ../applications/science/misc/nextflow {}; # aspera = callPackage ../tools/networking/aspera {}; # bbcp = callPackage ../tools/networking/bbcp {}; # ncbi-vdb = callPackage ../applications/science/biology/ncbi-vdb {}; - # nextflow = callPackage ../applications/science/misc/nextflow {}; # ngs = callPackage ../applications/science/biology/ngs {}; # seqlib = callPackage ../applications/science/biology/seqlib {}; # sra-tools = callPackage ../applications/science/biology/sra-tools {}; # tsunami-udp = callPackage ../tools/networking/tsunami-udp {}; # udpcast = callPackage ../tools/networking/udpcast {}; # udr = callPackage ../tools/networking/udr {}; - python36Packages = callPackage ./python-packages.nix {}; + # python36Packages = callPackage ./python-packages.nix {}; # nodejs = hiPrio nodejs-6_x; # nodePackages_6_x = callPackage ../development/node-packages/default-v6.nix { # nodejs = pkgs.nodejs-6_x; @@ -39,44 +36,45 @@ let }; containerReadyPkgs = { - bcftools = callPackage ../applications/science/biology/bcftools {}; - bedtools = callPackage ../applications/science/biology/bedtools {}; - bowtie2 = callPackage ../applications/science/biology/bowtie2 {}; - bwa = callPackage ../applications/science/biology/bwa {}; - fastqc = callPackage ../applications/science/biology/fastqc {}; - freebayes = callPackage ../applications/science/biology/freebayes {}; - kmc = callPackage ../applications/science/biology/kmc {}; - mrbayes = callPackage ../applications/science/biology/mrbayes {}; - paml- = callPackage ../applications/science/biology/paml {}; - picard-tools = callPackage ../applications/science/biology/picard-tools {}; - plink = callPackage ../applications/science/biology/plink {}; - plink-ng = callPackage ../applications/science/biology/plink-ng {}; - psmc = callPackage ../applications/science/biology/psmc {}; - seqbility = callPackage ../applications/science/biology/seqbility {}; - nextflow = callPackage ../applications/science/misc/nextflow {}; - msmc = callPackage ../applications/science/biology/msmc {}; - msmc-bin = callPackage ../applications/science/biology/msmc-bin {}; - shapeit-bin = callPackage ../applications/science/biology/shapeit-bin {}; - msmc2 = callPackage ../applications/science/biology/msmc2 {}; - msmc-tools = callPackage ../applications/science/biology/msmc-tools {}; - htslib = callPackage ../development/libraries/science/biology/htslib {}; - samtools = callPackage ../applications/science/biology/samtools {}; - seqtk = callPackage ../applications/science/biology/seqtk {}; - trimmomatic = callPackage ../applications/science/biology/trimmomatic {}; - }; - - customEnvs = { - shell = (import shellDir).env; + # bcftools = callPackage ../applications/science/biology/bcftools {}; + # bedtools = callPackage ../applications/science/biology/bedtools {}; + # bowtie2 = callPackage ../applications/science/biology/bowtie2 {}; + # bwa = callPackage ../applications/science/biology/bwa {}; + # fastqc = callPackage ../applications/science/biology/fastqc {}; + # freebayes = callPackage ../applications/science/biology/freebayes {}; + # kmc = callPackage ../applications/science/biology/kmc {}; + # mrbayes = callPackage ../applications/science/biology/mrbayes {}; + # paml- = callPackage ../applications/science/biology/paml {}; + # picard-tools = callPackage ../applications/science/biology/picard-tools {}; + # plink = callPackage ../applications/science/biology/plink {}; + # plink-ng = callPackage ../applications/science/biology/plink-ng {}; + # psmc = callPackage ../applications/science/biology/psmc {}; + # seqbility = callPackage ../applications/science/biology/seqbility {}; + # nextflow = callPackage ../applications/science/misc/nextflow {}; + # msmc = callPackage ../applications/science/biology/msmc {}; + # msmc-bin = callPackage ../applications/science/biology/msmc-bin {}; + # shapeit-bin = callPackage ../applications/science/biology/shapeit-bin {}; + # msmc2 = callPackage ../applications/science/biology/msmc2 {}; + # msmc-tools = callPackage ../applications/science/biology/msmc-tools {}; + # htslib = callPackage ../development/libraries/science/biology/htslib {}; + # samtools = callPackage ../applications/science/biology/samtools {}; + # seqtk = callPackage ../applications/science/biology/seqtk {}; + # trimmomatic = callPackage ../applications/science/biology/trimmomatic {}; }; - allPkgs = pkgs // customPkgs // containerReadyPkgs // customEnvs; + # customEnvs = { + # # shell = (import shellDir).env; + # }; - utils = { - containerReadyPkgs = containerReadyPkgs; - dockerTar = callPackage ./dockerTar.nix { inherit timestamp; pkg=allPkgs."${pkg}"; shellDir=(builtins.toPath shellDir); }; - nodePackages = customPkgs.nodePackages_6_x; - }; + # allPkgs = pkgs // customPkgs // containerReadyPkgs // customEnvs; - self = allPkgs // utils; + # utils = { + # source = source; + # containerReadyPkgs = containerReadyPkgs; + # dockerTar = callPackage ./dockerTar.nix { inherit timestamp; pkg=allPkgs."${pkg}"; shellDir=(builtins.toPath shellDir); }; + # nodePackages = customPkgs.nodePackages_6_x; + # }; + # self = allPkgs // utils; + self = pkgs // customPkgs; in self