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-rw-r--r--test-tnpair.nix2
-rw-r--r--test.nix2
-rw-r--r--tools/samtools-faidx.nix4
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
'';
}