From d3c9cf212e1d656e1f7cd256bdd1e1f9a2d12352 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 30 Nov 2020 08:20:28 +1100
Subject: gridss.assemble: fix workdir manipulation
---
tools/gridss-assemble.nix | 13 +++++++------
1 file changed, 7 insertions(+), 6 deletions(-)
(limited to 'tools')
diff --git a/tools/gridss-assemble.nix b/tools/gridss-assemble.nix
index f0a2693..9e51cab 100644
--- a/tools/gridss-assemble.nix
+++ b/tools/gridss-assemble.nix
@@ -40,7 +40,7 @@ assert (homoRef);
stage rec {
name = "gridss-assemble";
- buildInputs = with pkgs; [ jre bwa rsync ];
+ buildInputs = with pkgs; [ jre bwa ];
outputs = [ "out" "work" ];
buildCommand = ''
TMPDIR=$(pwd)
@@ -50,24 +50,25 @@ stage rec {
ln -s $f
done
${concatMapStringsSep "\n" linkInput inputs}
- ${concatMapStringsSep "\n" (w: "rsync -a --ignore-existing ${w}/ ./") workdirs}
+ mkdir out.gridss.working
+ ${concatMapStringsSep "\n" (w: "cp -r ${w}/* ./out.gridss.working") workdirs}
+ chmod -R u+rwX out.gridss.working
java -Xmx${heapSize} -Dsamjdk.create_index=true \
-cp ${bionix.gridss.jar} gridss.AssembleBreakends \
VERBOSITY=WARNING \
REFERENCE_SEQUENCE=ref.fa \
${concatMapStringsSep " " (i: "INPUT='${i}'") inputs} \
WORKER_THREADS=$NIX_BUILD_CORES \
- OUTPUT=$out \
+ OUTPUT=out \
${optionalString (config != null) ("OPTIONS_FILE=" + bionix.gridss.gridssConfig config)} \
WORKING_DIR=$TMPDIR/ \
TMP_DIR=$TMPDIR/ \
${optionalString (jobIndex != null) "JOB_INDEX=${toString jobIndex}"} \
${optionalString (jobIndex != null) "JOB_NODES=${toString jobNodes}"} \
${optionalString (flags != null) flags}
- rm -rf tmp
+ [ -e out ] && cp -r out $out
touch $out
- cp -r $TMPDIR $work
- chmod u+rwX -R $work
+ cp -r out.gridss.working $work
'';
passthru.filetype = filetype.bam { ref = ref; sorting = sort.name {}; };
passthru.multicore = true;
--
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