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Replace oracle specific _JAVA_OPTIONS to portable JAVA_TOOLS_OPTIONS

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This commit is contained in:
James Fellows Yates 2022-06-03 14:20:39 +02:00
parent 7353fb257d
commit df0429ce9d
1 changed files with 13 additions and 13 deletions
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8
conf/pipeline/eager/eva.config
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@ -9,7 +9,7 @@ params {
// Specific nf-core/eager process configuration // Specific nf-core/eager process configuration
process { process {
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
maxRetries = 2 maxRetries = 2
@ -192,7 +192,7 @@ process {
withName:get_software_versions { withName:get_software_versions {
cache = false cache = false
clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" } clusterOptions = { "-S /bin/bash -V -l h=!(bionode06)" }
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1' beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1 -Xmx512m"; export OPENBLAS_NUM_THREADS=1; export OMP_NUM_THREADS=1'
clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" } clusterOptions = { "-S /bin/bash -V -l h_vmem=${(task.memory.toMega())}M" }
errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' } errorStrategy = { task.exitStatus in [1,143,137,104,134,139,140] ? 'retry' : 'finish' }
} }
@ -226,7 +226,7 @@ profiles {
process { process {
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
maxRetries = 2 maxRetries = 2
@ -404,7 +404,7 @@ profiles {
process { process {
beforeScript = 'export _JAVA_OPTIONS="-XX:ParallelGCThreads=1"' beforeScript = 'export JAVA_TOOL_OPTIONS="-XX:ParallelGCThreads=1"'
maxRetries = 2 maxRetries = 2