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

---
 tools/samtools-faidx.nix | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

(limited to 'tools')

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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