From e7cd661d1c5fb4135e3d436e151294e26aef9127 Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Mon, 29 Oct 2018 15:33:53 +1100 Subject: Split gridss into constituents Wrap each individual command for GRIDSS so that bionix executed the pipeline rather than GRIDSS. This patch introduces a "call" function that executed the whole pipeline in bionix on an arbitrary BAM file. Resolves #10. --- tools/gridss-callVariants.nix | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) (limited to 'tools/gridss-callVariants.nix') diff --git a/tools/gridss-callVariants.nix b/tools/gridss-callVariants.nix index 799c930..416eb7c 100644 --- a/tools/gridss-callVariants.nix +++ b/tools/gridss-callVariants.nix @@ -23,10 +23,6 @@ assert (length (unique refs) == 1); stdenv.mkDerivation rec { name = "gridss-callVariants"; buildInputs = [ jre R bwa ]; - jar = fetchurl { - url = "https://github.com/PapenfussLab/gridss/releases/download/v2.0.0/gridss-2.0.0-gridss-jar-with-dependencies.jar"; - sha256 = "01srl3qvv060whqg1y1fpxjc5cwga5wscs1bmf1v3z87dignra7k"; - }; buildCommand = '' ln -s ${ref} ref.fa ln -s ${bionix.samtools.faidx faidxAttrs ref} ref.fa.fai @@ -41,7 +37,7 @@ stdenv.mkDerivation rec { -Dsamjdk.use_async_io_write_samtools=true \ -Dsamjdk.use_async_io_write_tribble=true \ -Dgridss.gridss.output_to_temp_file=true \ - -cp ${jar} gridss.CallVariants \ + -cp ${bionix.gridss.jar} gridss.CallVariants \ WORKER_THREADS=$NIX_BUILD_CORES \ TMP_DIR=. \ WORKING_DIR=. \ -- cgit v1.2.3