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

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Justin Bedő 2026-03-01 22:28:49 +00:00 committed by GitHub
commit 73a2e8631b
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3 changed files with 15 additions and 13 deletions

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@ -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";

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@ -686,6 +686,7 @@ with lib.maintainers;
members = [
b-rodrigues
bcdarwin
jamespeapen
jbedo
kupac
];

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@ -385,6 +385,7 @@ let
data_table = [ jbedo ];
BiocManager = [ jbedo ];
ggplot2 = [ jbedo ];
iscream = [ jamespeapen ];
svaNUMT = [ jbedo ];
svaRetro = [ jbedo ];
StructuralVariantAnnotation = [ jbedo ];
@ -3136,19 +3137,13 @@ let
'';
});
iscream =
let
# 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 ];
});
iscream = old.iscream.overrideAttrs (attrs: {
# https://huishenlab.github.io/iscream/articles/htslib.html
# Rhtslib (in LinkingTo) is not needed if we provide a proper htslib
propagatedBuildInputs =
builtins.filter (el: el != pkgs.rPackages.Rhtslib) attrs.propagatedBuildInputs
++ [ pkgs.htslib ];
});
torch = old.torch.overrideAttrs (attrs: {
preConfigure = ''