Unverified Commit 73a2e863 authored by Justin Bedő's avatar Justin Bedő Committed by GitHub
Browse files

rPackages.iscream: use pkgs.htslib without libdeflate override (#494840)

parents 9611501b d2596d01

maintainers/maintainer-list.nix

+6 −0
Original line number Diff line number Diff line
@@ -11835,6 +11835,12 @@ 
    github = "james-atkins";

    githubId = 9221409;

  };

  jamespeapen = {

    name = "James Eapen";

    email = "james.eapen@vai.org";

    github = "jamespeapen";

    githubId = 39574560;

  };

  jamesward = {

    email = "james@jamesward.com";

    name = "James Ward";

maintainers/team-list.nix

+1 −0
Original line number Diff line number Diff line
@@ -686,6 +686,7 @@ with lib.maintainers; 
    members = [

      b-rodrigues

      bcdarwin

      jamespeapen

      jbedo

      kupac

    ];

pkgs/development/r-modules/default.nix

+8 −13
Original line number Diff line number Diff line
@@ -385,6 +385,7 @@ let 
    data_table = [ jbedo ];

    BiocManager = [ jbedo ];

    ggplot2 = [ jbedo ];

    iscream = [ jamespeapen ];

    svaNUMT = [ jbedo ];

    svaRetro = [ jbedo ];

    StructuralVariantAnnotation = [ jbedo ];
@@ -3136,18 +3137,12 @@ let 
      '';

    });



    iscream =

      let

    iscream = old.iscream.overrideAttrs (attrs: {

      # https://huishenlab.github.io/iscream/articles/htslib.html

        htslib-deflate = pkgs.htslib.overrideAttrs (attrs: {

          buildInputs = attrs.buildInputs ++ [ pkgs.libdeflate ];

        });

      in

      old.iscream.overrideAttrs (attrs: {

      # Rhtslib (in LinkingTo) is not needed if we provide a proper htslib

      propagatedBuildInputs =

        builtins.filter (el: el != pkgs.rPackages.Rhtslib) attrs.propagatedBuildInputs

          ++ [ htslib-deflate ];

        ++ [ pkgs.htslib ];

    });



    torch = old.torch.overrideAttrs (attrs: {