1 files changed, 27 insertions, 0 deletions
diff --git a/tools/hisat2-index.nix b/tools/hisat2-index.nix
new file mode 100644
index 0000000..82935eb
--- /dev/null
+++ b/tools/hisat2-index.nix
@@ -0,0 +1,27 @@
+{ bionix
+, gtf ? null
+, flags ? null
+, extractSpliceSitesAttrs ? {}
+, extractExonsAttrs ? {}
+}:
+
+ref:
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "hisat2-index" { fa = _: true; } ref);
+
+stage {
+  name = "hisat2-index";
+  buildInputs = with pkgs; [ hisat2 ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    mkdir $out
+    hisat2-build -p $NIX_BUILD_CORES ${optionalString (flags != null) flags} \
+      ${optionalString (gtf != null) "--ss ${hisat2.extractSpliceSites extractSpliceSitesAttrs gtf} --exon ${hisat2.extractExons extractExonsAttrs gtf}"} \
+      ref.fa $out/
+  '';
+  passthru.multicore = true;
+}