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| author | l-d-s <distefano.l@wehi.edu.au> | 2018-09-24 12:04:51 +1000 |
|---|---|---|
| committer | l-d-s <distefano.l@wehi.edu.au> | 2018-09-24 12:04:51 +1000 |
| commit | 9c99509719704112c786c194f715c64aaa5b03de (patch) | |
| tree | 0dca0ee2cac04564b701835dd3ff69b1c94ea8bf | |
| parent | 1e4495d2a6d322c190aedce48d5c31b36e210c70 (diff) | |
Working test-tnpair
| -rw-r--r-- | test-tnpair.nix | 2 | ||||
| -rw-r--r-- | test.nix | 2 | ||||
| -rw-r--r-- | 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; }; @@ -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 ''; } |