rPackages.iscream: fix build and optimize

- Add missing build inputs
 - Compile htslib with libdeflate
 - Remove superfluous Rhtslib dependency

pkgs/development/r-modules/default.nix

@@ -610,6 +610,10 @@ let
       libpng.dev
     ];
     iBMQ = [ pkgs.gsl ];
+    iscream = with pkgs; [
+      pkg-config
+      which
+    ];
     jack = [ pkgs.pkg-config ];
     JavaGD = [ pkgs.jdk ];
     jpeg = [ pkgs.libjpeg.dev ];
@@ -1185,6 +1189,11 @@ let
     chebpol = [ pkgs.pkg-config ];
     baseline = [ pkgs.lapack ];
     eds = [ pkgs.zlib.dev ];
+    iscream = with pkgs; [
+      bzip2.dev
+      xz.dev
+      zlib.dev
+    ];
     pgenlibr = [ pkgs.zlib.dev ];
     fftw = [ pkgs.pkg-config ];
     gdtools = [ pkgs.pkg-config ];
@@ -3010,6 +3019,20 @@ 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 ];
+      });
+
     torch = old.torch.overrideAttrs (attrs: {
       preConfigure = ''
         patchShebangs configure