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Fix stackoverflow issue with wich custom nix-channel and disable pack…
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@bmpvieira
bmpvieira committed Jan 7, 2019
1 parent e31ff5e commit cdda264
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Showing 3 changed files with 49 additions and 55 deletions.
11 changes: 6 additions & 5 deletions default.nix
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
{ system ? builtins.currentSystem, pkg ? null, timestamp ? "1970-01-01T00:00:01Z" }:
{ system ? builtins.currentSystem }:
let
nixpkgs = import <nixpkgs> { inherit system; };
makeOverridable = nixpkgs.stdenv.lib.makeOverridable;
pkgs = import ./pkgs/top-level/all-packages.nix;
# nixpkgs = import <nixpkgs> { 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
9 changes: 2 additions & 7 deletions nixsrc.json
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Original file line number Diff line number Diff line change
@@ -1,9 +1,4 @@
{
"version": "17.09",
"origin": {
"owner": "NixOS",
"repo": "nixpkgs",
"rev": "39cd40f7bea40116ecb756d46a687bfd0d2e550e",
"sha256": "0kpx4h9p1lhjbn1gsil111swa62hmjs9g93xmsavfiki910s73sh"
}
"version": "18.09",
"sha256": "1ib96has10v5nr6bzf7v8kw7yzww8zanxgw2qi1ll1sbv6kj6zpd"
}
84 changes: 41 additions & 43 deletions pkgs/top-level/all-packages.nix
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Original file line number Diff line number Diff line change
@@ -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; };

Expand All @@ -21,62 +18,63 @@ 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;
# };
};

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

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