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rPackages.iscream: use pkgs.htslib without libdeflate override (#494840)
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commit
73a2e8631b
3 changed files with 15 additions and 13 deletions
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@ -11835,6 +11835,12 @@
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github = "james-atkins";
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githubId = 9221409;
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};
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jamespeapen = {
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name = "James Eapen";
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email = "james.eapen@vai.org";
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github = "jamespeapen";
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githubId = 39574560;
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};
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jamesward = {
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email = "james@jamesward.com";
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name = "James Ward";
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@ -686,6 +686,7 @@ with lib.maintainers;
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members = [
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b-rodrigues
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bcdarwin
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jamespeapen
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jbedo
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kupac
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];
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@ -385,6 +385,7 @@ let
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data_table = [ jbedo ];
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BiocManager = [ jbedo ];
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ggplot2 = [ jbedo ];
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iscream = [ jamespeapen ];
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svaNUMT = [ jbedo ];
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svaRetro = [ jbedo ];
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StructuralVariantAnnotation = [ jbedo ];
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@ -3136,19 +3137,13 @@ let
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'';
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});
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iscream =
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let
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# https://huishenlab.github.io/iscream/articles/htslib.html
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htslib-deflate = pkgs.htslib.overrideAttrs (attrs: {
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buildInputs = attrs.buildInputs ++ [ pkgs.libdeflate ];
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});
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in
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old.iscream.overrideAttrs (attrs: {
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# Rhtslib (in LinkingTo) is not needed if we provide a proper htslib
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propagatedBuildInputs =
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builtins.filter (el: el != pkgs.rPackages.Rhtslib) attrs.propagatedBuildInputs
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++ [ htslib-deflate ];
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});
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iscream = old.iscream.overrideAttrs (attrs: {
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# https://huishenlab.github.io/iscream/articles/htslib.html
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# Rhtslib (in LinkingTo) is not needed if we provide a proper htslib
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propagatedBuildInputs =
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builtins.filter (el: el != pkgs.rPackages.Rhtslib) attrs.propagatedBuildInputs
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++ [ pkgs.htslib ];
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});
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torch = old.torch.overrideAttrs (attrs: {
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preConfigure = ''
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