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mosdepth: convert to buildNimPackage

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This commit is contained in:
Emery Hemingway 2021-09-02 18:35:32 +02:00
parent 114ca1a5a8
commit 323c503cba
4 changed files with 29 additions and 26 deletions
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30
pkgs/applications/science/biology/mosdepth/default.nix
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@ -1,23 +1,9 @@
{lib, stdenv, fetchFromGitHub, nim, htslib, pcre}:
{lib, nimPackages, fetchFromGitHub, pcre}:
let
hts-nim = fetchFromGitHub {
owner = "brentp";
repo = "hts-nim";
rev = "v0.3.4";
sha256 = "0670phk1bq3l9j2zaa8i5wcpc5dyfrc0l2a6c21g0l2mmdczffa7";
};
docopt = fetchFromGitHub {
owner = "docopt";
repo = "docopt.nim";
rev = "v0.6.7";
sha256 = "1ga7ckg21fzwwvh26jp2phn2h3pvkn8g8sm13dxif33rp471bv37";
};
in stdenv.mkDerivation rec {
nimPackages.buildNimPackage rec {
pname = "mosdepth";
version = "0.3.2";
nimBinOnly = true;
src = fetchFromGitHub {
owner = "brentp";
@ -26,15 +12,7 @@ in stdenv.mkDerivation rec {
sha256 = "sha256-uui4yC7ok+pvbXVKfBVsAarH40fnH4fnP8P4uzOqztQ=";
};
nativeBuildInputs = [ nim ];
buildInputs = [ htslib pcre ];
buildPhase = ''
HOME=$TMPDIR
nim -p:${hts-nim}/src -p:${docopt}/src c --nilseqs:on -d:release mosdepth.nim
'';
installPhase = "install -Dt $out/bin mosdepth";
buildInputs = with nimPackages; [ docopt hts-nim pcre ];
meta = with lib; {
description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing";

8
pkgs/development/nim-packages/docopt/default.nix Normal file
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@ -0,0 +1,8 @@
{ fetchFromGitHub }:
fetchFromGitHub {
owner = "docopt";
repo = "docopt.nim";
rev = "v0.6.7";
sha256 = "1ga7ckg21fzwwvh26jp2phn2h3pvkn8g8sm13dxif33rp471bv37";
}

13
pkgs/development/nim-packages/hts-nim/default.nix Normal file
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@ -0,0 +1,13 @@
{ buildNimPackage, fetchFromGitHub, htslib }:
buildNimPackage rec {
pname = "hts-nim";
version = "0.3.4";
src = fetchFromGitHub {
owner = "brentp";
repo = pname;
rev = "v${version}";
sha256 = "0670phk1bq3l9j2zaa8i5wcpc5dyfrc0l2a6c21g0l2mmdczffa7";
};
propagatedBuildInputs = [ htslib ];
}

4
pkgs/top-level/nim-packages.nix
View file

@ -16,10 +16,14 @@ lib.makeScope newScope (self:
chroma = callPackage ../development/nim-packages/chroma { };
docopt = callPackage ../development/nim-packages/docopt { };
flatty = callPackage ../development/nim-packages/flatty { };
frosty = callPackage ../development/nim-packages/frosty { };
hts-nim = callPackage ../development/nim-packages/hts-nim { };
jester = callPackage ../development/nim-packages/jester { };
jsonschema = callPackage ../development/nim-packages/jsonschema { };