diff options
| author | Justin Bedo <cu@cua0.org> | 2018-10-29 15:33:53 +1100 |
|---|---|---|
| committer | Justin Bedo <cu@cua0.org> | 2018-10-29 15:36:33 +1100 |
| commit | e7cd661d1c5fb4135e3d436e151294e26aef9127 (patch) | |
| tree | 71ef7647d15d57bc2db2cf8ec532da794fddb2fa /tools/gridss-callVariants.nix | |
| parent | 8fb986fd88705fc01be7145b04fa229092c1e69e (diff) | |
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.
Diffstat (limited to 'tools/gridss-callVariants.nix')
| -rw-r--r-- | tools/gridss-callVariants.nix | 6 |
1 files changed, 1 insertions, 5 deletions
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=. \ |