From f416c145204765a1566782f0ff384d3f65d6ed35 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Fri, 2 Nov 2018 15:35:22 +1100
Subject: kallisto: init

---
 lib/references.nix | 22 ++++++++++++++++++++++
 lib/types.nix      |  3 ++-
 2 files changed, 24 insertions(+), 1 deletion(-)

(limited to 'lib')

diff --git a/lib/references.nix b/lib/references.nix
index 498cfd9..bdeefa6 100755
--- a/lib/references.nix
+++ b/lib/references.nix
@@ -46,6 +46,28 @@ rec {
       '';
       passthru.filetype = filetype.vcf { ref = seq; };
     };
+    ensembl = {
+      cdna = stdenvNoCC.mkDerivation rec {
+        name = "ensembl-grch38-cdna-${version}";
+        version = "94";
+        src = fetchurl {
+          url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz";
+          sha256 = "1fc5d6p2wlwsm49wnmxmm3byjx5jvr6z9fpzrq7v7fpb086adl0h";
+        };
+        buildCommand = "gunzip < $src > $out";
+        passthru.filetype = filetype.fa {};
+      };
+      ncrna = stdenvNoCC.mkDerivation rec {
+        name = "ensembl-grch38-ncrna-${version}";
+        version = "94";
+        src = fetchurl {
+          url = "ftp://ftp.ensembl.org/pub/release-${version}/fasta/homo_sapiens/ncrna/Homo_sapiens.GRCh38.ncrna.fa.gz";
+          sha256 = "1cpasykwriila52nqgvw6d3mjyh6d9qi613hvhn4h1dxkqzgnjff";
+        };
+        buildCommand = "gunzip < $src > $out";
+        passthru.filetype = filetype.fa {};
+      };
+    };
   };
 
   grcm38 = grcm38-p6;
diff --git a/lib/types.nix b/lib/types.nix
index 4dbc6ff..ef9b1b7 100644
--- a/lib/types.nix
+++ b/lib/types.nix
@@ -21,7 +21,8 @@ let
 
 in
 rec {
-  matchFiletype = sym: y: x: if x ? filetype then match x.filetype (defError (idft sym) y filetype) else abort "unknown filetype for ${sym}";
+  matchFiletype = sym: y: x: if x ? filetype then matchFiletype' sym y x.filetype else abort "unknown filetype for ${sym}";
+  matchFiletype' = sym: y: x: match x (defError (idft sym) y filetype);
   filetype = make-type "filetype" {
     fa = {};
     fq = {};
-- 
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