star: init

1 files changed, 33 insertions, 0 deletions

diff --git a/tools/star-index.nix b/tools/star-index.nix
new file mode 100644
index 0000000..4bc8399
--- /dev/null
+++ b/tools/star-index.nix
@@ -0,0 +1,33 @@
+{ bionix
+, gtf
+, flags ? null
+, extractSpliceSitesAttrs ? {}
+, extractExonsAttrs ? {}
+, overhang ? 100
+}:
+
+ref:
+
+with bionix;
+with lib;
+with types;
+
+assert (matchFiletype "star-index" { fa = _: true; } ref);
+
+stage {
+  name = "star-index";
+  buildInputs = with pkgs; [ star ];
+  buildCommand = ''
+    ln -s ${ref} ref.fa
+    mkdir $out
+    STAR --runMode genomeGenerate \
+      --runThreadN $NIX_BUILD_CORES \
+      --sjdbGTFfile ${gtf} \
+      --genomeDir $out \
+      --genomeFastaFiles ${ref} \
+      --sjdbOverhang ${toString overhang} \
+      ${optionalString (flags != null) flags}
+  '';
+  passthru.multicore = true;
+  stripStorePaths = false;
+}