From 9c99509719704112c786c194f715c64aaa5b03de Mon Sep 17 00:00:00 2001
From: l-d-s <distefano.l@wehi.edu.au>
Date: Mon, 24 Sep 2018 12:04:51 +1000
Subject: Working test-tnpair

---
 test-tnpair.nix          | 2 +-
 test.nix                 | 2 +-
 tools/samtools-faidx.nix | 4 +++-
 3 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/test-tnpair.nix b/test-tnpair.nix
index 371ef81..40cb442 100644
--- a/test-tnpair.nix
+++ b/test-tnpair.nix
@@ -4,7 +4,7 @@ with pkgs;
 with lib;
 
 let
-  ref = ../bioshake/examples/ref.fa;
+  ref = ./example/ref.fa;
   alignWithRG = rg: callPackage ./tools/bwa.nix { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
   sort = callPackage ./tools/samtools-sort.nix { };
   callVariants = callPackage ./tools/strelka.nix { inherit ref; };
diff --git a/test.nix b/test.nix
index 6c158c6..3bfaed6 100644
--- a/test.nix
+++ b/test.nix
@@ -4,7 +4,7 @@ with pkgs;
 with lib;
 
 let
-  ref = ../bioshake/examples/ref.fa;
+  ref = ./example/ref.fa;
   alignWithRG = rg: callPackage ./tools/bwa.nix { inherit ref; flags = "-R'@RG\\tID:${rg}\\tSM:${rg}'";};
   sort = callPackage ./tools/samtools-sort.nix { };
   callVariants = callPackage ./tools/platypus.nix { inherit ref; };
diff --git a/tools/samtools-faidx.nix b/tools/samtools-faidx.nix
index 0dc03ee..a399857 100644
--- a/tools/samtools-faidx.nix
+++ b/tools/samtools-faidx.nix
@@ -13,6 +13,8 @@ stdenv.mkDerivation {
   name = "samtools-faidx";
   buildInputs = [ samtools ];
   buildCommand = ''
-    samtools faidx ${optionalString (flags != null) flags} ${input} > $out
+    ln -s ${input} input.fasta
+    samtools faidx ${optionalString (flags != null) flags} input.fasta
+    cp input.fasta.fai $out
   '';
 }
-- 
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