parent
3d8e0fe114
commit
24d7820165
GPG Key ID:
9893DA236405AF57
|
|
@ -0,0 +1,41 @@
|
|||
{
|
||||
"nodes": {
|
||||
"flake-utils": {
|
||||
"locked": {
|
||||
"lastModified": 1634851050,
|
||||
"narHash": "sha256-N83GlSGPJJdcqhUxSCS/WwW5pksYf3VP1M13cDRTSVA=",
|
||||
"owner": "numtide",
|
||||
"repo": "flake-utils",
|
||||
"rev": "c91f3de5adaf1de973b797ef7485e441a65b8935",
|
||||
"type": "github"
|
||||
},
|
||||
"original": {
|
||||
"owner": "numtide",
|
||||
"repo": "flake-utils",
|
||||
"type": "github"
|
||||
}
|
||||
},
|
||||
"nixpkgs": {
|
||||
"locked": {
|
||||
"lastModified": 1635865339,
|
||||
"narHash": "sha256-fmI8PxMmL7WXV/O8m6vT9/yW42buxvAYeRNpcABvnKs=",
|
||||
"owner": "NixOS",
|
||||
"repo": "nixpkgs",
|
||||
"rev": "26a56abd090ec5c8f4c6c9e1189fbfa4bcb8db3f",
|
||||
"type": "github"
|
||||
},
|
||||
"original": {
|
||||
"id": "nixpkgs",
|
||||
"type": "indirect"
|
||||
}
|
||||
},
|
||||
"root": {
|
||||
"inputs": {
|
||||
"flake-utils": "flake-utils",
|
||||
"nixpkgs": "nixpkgs"
|
||||
}
|
||||
}
|
||||
},
|
||||
"root": "root",
|
||||
"version": 7
|
||||
}
|
||||
|
|
@ -0,0 +1,13 @@
|
|||
{
|
||||
description = ''
|
||||
locigenesis is a tool that generates a human T-cell receptor (TCR), runs
|
||||
it through a sequence reader simulation tool and extracts CDR3.
|
||||
'';
|
||||
|
||||
inputs.flake-utils.url = "github:numtide/flake-utils";
|
||||
|
||||
outputs = { self, nixpkgs, flake-utils }:
|
||||
flake-utils.lib.eachDefaultSystem (system:
|
||||
let pkgs = nixpkgs.legacyPackages.${system};
|
||||
in { devShell = import ./shell.nix { inherit pkgs; }; });
|
||||
}
|
||||
|
|
@ -1,26 +0,0 @@
|
|||
{
|
||||
"niv": {
|
||||
"branch": "master",
|
||||
"description": "Easy dependency management for Nix projects",
|
||||
"homepage": "https://github.com/nmattia/niv",
|
||||
"owner": "nmattia",
|
||||
"repo": "niv",
|
||||
"rev": "af958e8057f345ee1aca714c1247ef3ba1c15f5e",
|
||||
"sha256": "1qjavxabbrsh73yck5dcq8jggvh3r2jkbr6b5nlz5d9yrqm9255n",
|
||||
"type": "tarball",
|
||||
"url": "https://github.com/nmattia/niv/archive/af958e8057f345ee1aca714c1247ef3ba1c15f5e.tar.gz",
|
||||
"url_template": "https://github.com/<owner>/<repo>/archive/<rev>.tar.gz"
|
||||
},
|
||||
"nixpkgs": {
|
||||
"branch": "release-20.09",
|
||||
"description": "Nix Packages collection",
|
||||
"homepage": "",
|
||||
"owner": "NixOS",
|
||||
"repo": "nixpkgs",
|
||||
"rev": "359e6542e1d41eb18df55c82bdb08bf738fae2cf",
|
||||
"sha256": "05v28njaas9l26ibc6vy6imvy7grbkli32bmv0n32x6x9cf68gf9",
|
||||
"type": "tarball",
|
||||
"url": "https://github.com/NixOS/nixpkgs/archive/359e6542e1d41eb18df55c82bdb08bf738fae2cf.tar.gz",
|
||||
"url_template": "https://github.com/<owner>/<repo>/archive/<rev>.tar.gz"
|
||||
}
|
||||
}
|
||||
174
nix/sources.nix
174
nix/sources.nix
|
|
@ -1,174 +0,0 @@
|
|||
# This file has been generated by Niv.
|
||||
|
||||
let
|
||||
|
||||
#
|
||||
# The fetchers. fetch_<type> fetches specs of type <type>.
|
||||
#
|
||||
|
||||
fetch_file = pkgs: name: spec:
|
||||
let
|
||||
name' = sanitizeName name + "-src";
|
||||
in
|
||||
if spec.builtin or true then
|
||||
builtins_fetchurl { inherit (spec) url sha256; name = name'; }
|
||||
else
|
||||
pkgs.fetchurl { inherit (spec) url sha256; name = name'; };
|
||||
|
||||
fetch_tarball = pkgs: name: spec:
|
||||
let
|
||||
name' = sanitizeName name + "-src";
|
||||
in
|
||||
if spec.builtin or true then
|
||||
builtins_fetchTarball { name = name'; inherit (spec) url sha256; }
|
||||
else
|
||||
pkgs.fetchzip { name = name'; inherit (spec) url sha256; };
|
||||
|
||||
fetch_git = name: spec:
|
||||
let
|
||||
ref =
|
||||
if spec ? ref then spec.ref else
|
||||
if spec ? branch then "refs/heads/${spec.branch}" else
|
||||
if spec ? tag then "refs/tags/${spec.tag}" else
|
||||
abort "In git source '${name}': Please specify `ref`, `tag` or `branch`!";
|
||||
in
|
||||
builtins.fetchGit { url = spec.repo; inherit (spec) rev; inherit ref; };
|
||||
|
||||
fetch_local = spec: spec.path;
|
||||
|
||||
fetch_builtin-tarball = name: throw
|
||||
''[${name}] The niv type "builtin-tarball" is deprecated. You should instead use `builtin = true`.
|
||||
$ niv modify ${name} -a type=tarball -a builtin=true'';
|
||||
|
||||
fetch_builtin-url = name: throw
|
||||
''[${name}] The niv type "builtin-url" will soon be deprecated. You should instead use `builtin = true`.
|
||||
$ niv modify ${name} -a type=file -a builtin=true'';
|
||||
|
||||
#
|
||||
# Various helpers
|
||||
#
|
||||
|
||||
# https://github.com/NixOS/nixpkgs/pull/83241/files#diff-c6f540a4f3bfa4b0e8b6bafd4cd54e8bR695
|
||||
sanitizeName = name:
|
||||
(
|
||||
concatMapStrings (s: if builtins.isList s then "-" else s)
|
||||
(
|
||||
builtins.split "[^[:alnum:]+._?=-]+"
|
||||
((x: builtins.elemAt (builtins.match "\\.*(.*)" x) 0) name)
|
||||
)
|
||||
);
|
||||
|
||||
# The set of packages used when specs are fetched using non-builtins.
|
||||
mkPkgs = sources: system:
|
||||
let
|
||||
sourcesNixpkgs =
|
||||
import (builtins_fetchTarball { inherit (sources.nixpkgs) url sha256; }) { inherit system; };
|
||||
hasNixpkgsPath = builtins.any (x: x.prefix == "nixpkgs") builtins.nixPath;
|
||||
hasThisAsNixpkgsPath = <nixpkgs> == ./.;
|
||||
in
|
||||
if builtins.hasAttr "nixpkgs" sources
|
||||
then sourcesNixpkgs
|
||||
else if hasNixpkgsPath && ! hasThisAsNixpkgsPath then
|
||||
import <nixpkgs> {}
|
||||
else
|
||||
abort
|
||||
''
|
||||
Please specify either <nixpkgs> (through -I or NIX_PATH=nixpkgs=...) or
|
||||
add a package called "nixpkgs" to your sources.json.
|
||||
'';
|
||||
|
||||
# The actual fetching function.
|
||||
fetch = pkgs: name: spec:
|
||||
|
||||
if ! builtins.hasAttr "type" spec then
|
||||
abort "ERROR: niv spec ${name} does not have a 'type' attribute"
|
||||
else if spec.type == "file" then fetch_file pkgs name spec
|
||||
else if spec.type == "tarball" then fetch_tarball pkgs name spec
|
||||
else if spec.type == "git" then fetch_git name spec
|
||||
else if spec.type == "local" then fetch_local spec
|
||||
else if spec.type == "builtin-tarball" then fetch_builtin-tarball name
|
||||
else if spec.type == "builtin-url" then fetch_builtin-url name
|
||||
else
|
||||
abort "ERROR: niv spec ${name} has unknown type ${builtins.toJSON spec.type}";
|
||||
|
||||
# If the environment variable NIV_OVERRIDE_${name} is set, then use
|
||||
# the path directly as opposed to the fetched source.
|
||||
replace = name: drv:
|
||||
let
|
||||
saneName = stringAsChars (c: if isNull (builtins.match "[a-zA-Z0-9]" c) then "_" else c) name;
|
||||
ersatz = builtins.getEnv "NIV_OVERRIDE_${saneName}";
|
||||
in
|
||||
if ersatz == "" then drv else
|
||||
# this turns the string into an actual Nix path (for both absolute and
|
||||
# relative paths)
|
||||
if builtins.substring 0 1 ersatz == "/" then /. + ersatz else /. + builtins.getEnv "PWD" + "/${ersatz}";
|
||||
|
||||
# Ports of functions for older nix versions
|
||||
|
||||
# a Nix version of mapAttrs if the built-in doesn't exist
|
||||
mapAttrs = builtins.mapAttrs or (
|
||||
f: set: with builtins;
|
||||
listToAttrs (map (attr: { name = attr; value = f attr set.${attr}; }) (attrNames set))
|
||||
);
|
||||
|
||||
# https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/lists.nix#L295
|
||||
range = first: last: if first > last then [] else builtins.genList (n: first + n) (last - first + 1);
|
||||
|
||||
# https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/strings.nix#L257
|
||||
stringToCharacters = s: map (p: builtins.substring p 1 s) (range 0 (builtins.stringLength s - 1));
|
||||
|
||||
# https://github.com/NixOS/nixpkgs/blob/0258808f5744ca980b9a1f24fe0b1e6f0fecee9c/lib/strings.nix#L269
|
||||
stringAsChars = f: s: concatStrings (map f (stringToCharacters s));
|
||||
concatMapStrings = f: list: concatStrings (map f list);
|
||||
concatStrings = builtins.concatStringsSep "";
|
||||
|
||||
# https://github.com/NixOS/nixpkgs/blob/8a9f58a375c401b96da862d969f66429def1d118/lib/attrsets.nix#L331
|
||||
optionalAttrs = cond: as: if cond then as else {};
|
||||
|
||||
# fetchTarball version that is compatible between all the versions of Nix
|
||||
builtins_fetchTarball = { url, name ? null, sha256 }@attrs:
|
||||
let
|
||||
inherit (builtins) lessThan nixVersion fetchTarball;
|
||||
in
|
||||
if lessThan nixVersion "1.12" then
|
||||
fetchTarball ({ inherit url; } // (optionalAttrs (!isNull name) { inherit name; }))
|
||||
else
|
||||
fetchTarball attrs;
|
||||
|
||||
# fetchurl version that is compatible between all the versions of Nix
|
||||
builtins_fetchurl = { url, name ? null, sha256 }@attrs:
|
||||
let
|
||||
inherit (builtins) lessThan nixVersion fetchurl;
|
||||
in
|
||||
if lessThan nixVersion "1.12" then
|
||||
fetchurl ({ inherit url; } // (optionalAttrs (!isNull name) { inherit name; }))
|
||||
else
|
||||
fetchurl attrs;
|
||||
|
||||
# Create the final "sources" from the config
|
||||
mkSources = config:
|
||||
mapAttrs (
|
||||
name: spec:
|
||||
if builtins.hasAttr "outPath" spec
|
||||
then abort
|
||||
"The values in sources.json should not have an 'outPath' attribute"
|
||||
else
|
||||
spec // { outPath = replace name (fetch config.pkgs name spec); }
|
||||
) config.sources;
|
||||
|
||||
# The "config" used by the fetchers
|
||||
mkConfig =
|
||||
{ sourcesFile ? if builtins.pathExists ./sources.json then ./sources.json else null
|
||||
, sources ? if isNull sourcesFile then {} else builtins.fromJSON (builtins.readFile sourcesFile)
|
||||
, system ? builtins.currentSystem
|
||||
, pkgs ? mkPkgs sources system
|
||||
}: rec {
|
||||
# The sources, i.e. the attribute set of spec name to spec
|
||||
inherit sources;
|
||||
|
||||
# The "pkgs" (evaluated nixpkgs) to use for e.g. non-builtin fetchers
|
||||
inherit pkgs;
|
||||
};
|
||||
|
||||
in
|
||||
mkSources (mkConfig {}) // { __functor = _: settings: mkSources (mkConfig settings); }
|
||||
|
|
@ -1,4 +1,4 @@
|
|||
{ sources ? import ./nix/sources.nix, pkgs ? import sources.nixpkgs { } }:
|
||||
{ pkgs ? import <nixpkgs> { } }:
|
||||
|
||||
with pkgs;
|
||||
|
||||
|
|
@ -6,8 +6,7 @@ let
|
|||
CuReSim = stdenv.mkDerivation rec {
|
||||
name = "CuReSim";
|
||||
version = "1.3";
|
||||
src = fetchzip {
|
||||
url =
|
||||
src = fetchzip { url =
|
||||
"http://www.pegase-biosciences.com/wp-content/uploads/2015/08/${name}${version}.zip";
|
||||
sha256 = "1hvlpgy4haqgqq52mkxhcl9i1fx67kgwi6f1mijvqzk0xff77hkp";
|
||||
stripRoot = true;
|
||||
|
|
|
|||
Loading…
Reference in New Issue