Merge branch 'master' of https://github.com/PapenfussLab/bionix

1 files changed, 22 insertions, 0 deletions

diff --git a/tools/kallisto-index.nix b/tools/kallisto-index.nix
new file mode 100644
index 0000000..33dfb80
--- /dev/null
+++ b/tools/kallisto-index.nix
@@ -0,0 +1,22 @@
+{bionix
+, nixpkgs
+, kmerSize ? 31
+, unique ? false}:
+
+with nixpkgs;
+with lib;
+with bionix.types;
+
+assert (kmerSize > 1);
+
+input:
+
+assert (matchFiletype input { fa = _: true; } input);
+
+stdenv.mkDerivation {
+  name = "kallisto-index";
+  buildInputs = [ kallisto ];
+  buildCommand = ''
+    kallisto index -k ${toString kmerSize} ${optionalString unique "--make-unique"} -i $out ${input}
+  '';
+}