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nextflow: fix trace+docker failure by reverting trace_cmd bash path

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This commit is contained in:
mulatta
2026-02-19 10:34:55 +09:00
parent 90a2ba07a9
commit bdc35de3a3
2 changed files with 22 additions and 6 deletions
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16
nixos/tests/nextflow.nix
View File

@@ -1,5 +1,7 @@
{ pkgs, ... }:
let
# This is the default image used by Nextflow if docker.enabled=true and no
# process.container is defined.
bash = pkgs.dockerTools.pullImage {
imageName = "quay.io/nextflow/bash";
imageDigest = "sha256:bea0e244b7c5367b2b0de687e7d28f692013aa18970941c7dd184450125163ac";
@@ -21,13 +23,17 @@ let
};
run-nextflow-pipeline = pkgs.writeShellApplication {
name = "run-nextflow-pipeline";
runtimeInputs = [ pkgs.nextflow ];
text = ''
export NXF_OFFLINE=true
for b in false true; do
echo "docker.enabled = $b" > nextflow.config
cat nextflow.config
nextflow run -ansi-log false ${hello}
for d in true false; do
for t in true false; do
rm -f nextflow.config; touch nextflow.config
echo "docker.enabled = $d" >> nextflow.config
echo "trace.enabled = $t" >> nextflow.config
echo "Testing docker=$d trace=$t"
nextflow run -ansi-log false ${hello}
echo "PASSED docker=$d trace=$t"
done
done
'';
};

12
pkgs/by-name/ne/nextflow/package.nix
View File

@@ -39,11 +39,21 @@ stdenv.mkDerivation (finalAttrs: {
# several locations so we fix that globally. However, when running inside
# a container, we actually *want* "/bin/bash". Thus the global fix needs
# to be reverted for this specific use case.
#
# Two code paths need the revert:
# 1. launcher (the command that invokes .command.run)
# 2. trace_cmd (the command inside .command.run's nxf_trace function
# that invokes .command.sh — see command-trace.txt template)
# Without the trace_cmd revert, trace+docker fails because the trace
# function tries to call /nix/store/.../bash inside the container.
# See https://github.com/NixOS/nixpkgs/issues/350183
substituteInPlace modules/nextflow/src/main/groovy/nextflow/executor/BashWrapperBuilder.groovy \
--replace-fail "['/bin/bash'," "['${bash}/bin/bash'," \
--replace-fail '? "/bin/bash"' '? "'${bash}'/bin/bash"' \
--replace-fail "if( containerBuilder ) {" "if( containerBuilder ) {
launcher = launcher.replaceFirst(\"/nix/store/.*/bin/bash\", \"/bin/bash\")"
launcher = launcher.replaceFirst(\"/nix/store/.*/bin/bash\", \"/bin/bash\")" \
--replace-fail "binding.trace_cmd = getTraceCommand(interpreter)" \
"binding.trace_cmd = containerBuilder != null ? getTraceCommand(interpreter).replaceFirst(\"/nix/store/.*/bin/bash\", \"/bin/bash\") : getTraceCommand(interpreter)"
'';
mitmCache = gradle.fetchDeps {