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- include required(classpath("application"))
- webservice {
- port = 8000
- }
- backend {
- default="SGE"
- providers {
- SGE {
- actor-factory = "cromwell.backend.impl.sfs.config.ConfigBackendLifecycleActorFactory"
- config {
- concurrent-job-limit = 10000
- runtime-attributes= """
- Int? cpu=1
- Int? memory=4
- """
- submit = """
- qsub \
- -terse \
- -V \
- -b n \
- -wd ${cwd} \
- -N ${job_name} \
- ${'-pe BWA ' + cpu} \
- ${'-l h_vmem=' + memory + "G"} \
- -o ${out} \
- -e ${err} \
- ${script}
- """
- kill = "qdel ${job_id}"
- check-alive = "qstat -j ${job_id}"
- job-id-regex = "(\\d+)"
- filesystems {
- localization: [
- "soft-link", "copy", "hard-link"
- ]
- local {
- caching {
- duplication-strategy: [ "soft-link", "copy", "hard-link" ]
- hashing-strategy: "file"
- }
- }
- }
- }
- }
- }
- }
- system {
- abort-jobs-on-terminate = true
- io {
- number-of-requests = 10
- per = 10 seconds
- number-of-attempts = 180
- }
- }
- call-caching {
- enabled = true
- invalidate-bad-cache-results = true
- }
- database {
- db.url = "jdbc:mysql://ourdatabase/cromwell_db?useSSL=false&rewriteBatchedStatements=true"
- db.user = "****"
- db.password = "****"
- db.driver = "com.mysql.jdbc.Driver"
- profile = "slick.jdbc.MySQLProfile$"
- }
- workflow-options {
- workflow-failure-mode = "ContinueWhilePossible"
- }
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