If the compressed tool file exists and the extracted folder exists without files, Roddy runs will fail.

dankwart-de commented 7 years ago

    1,4M Jul  5 10:35 cTools_ACEseqWorkflow:1.2.8-1_copyNumberEstimationWorkflow_170705_103552779.zip
     36K Jun 26 21:34 cTools_AlignmentAndQCWorkflows:1.1.39-0_bisulfiteWorkflow_170626_213432499.zip
    5,9K Jun 26 21:34 cTools_AlignmentAndQCWorkflows:1.1.39-0_exomePipeline_170626_213432499.zip
     88K Jun 26 21:34 cTools_AlignmentAndQCWorkflows:1.1.39-0_qcPipeline_170626_213432499.zip
    1,8M Jun 26 21:34 cTools_AlignmentAndQCWorkflows:1.1.39-0_qcPipelineTools_170626_213432499.zip
    4,1K Jun 26 21:34 cTools_COWorkflows:1.1.59-0_devel_170626_213432499.zip
     39K Jun 26 21:34 cTools_COWorkflows:1.1.59-0_tools_170626_213432499.zip
     39K Jun  9 18:03 cTools_COWorkflows:1.1.76-1_tools_170705_103632264.zip
    2,8K Jun 26 21:34 cTools_DefaultPlugin:1.0.33-1_roddyNativeTools_170626_213432499.zip
    3,5K Jun 26 21:34 cTools_DefaultPlugin:1.0.33-1_roddyTools_170626_213432499.zip
    3,5K Jul  5 21:17 cTools_DefaultPlugin:1.0.33-1_roddyTools_170705_211750327.zip
       0 Jul  5 10:36 dir_cTools_ACEseqWorkflow:1.2.8-1_copyNumberEstimationWorkflow_170705_103552779.zip
      35 Jun 26 21:34 dir_cTools_AlignmentAndQCWorkflows:1.1.39-0_bisulfiteWorkflow_170626_213432499.zip
      31 Jun 26 21:34 dir_cTools_AlignmentAndQCWorkflows:1.1.39-0_exomePipeline_170626_213432499.zip

dankwart-de commented 7 years ago

In addition, the logs are not very clear and helpful.

  [[ ${WRAPPED_SCRIPT-false} == false || ! -f ${WRAPPED_SCRIPT} ]] && startCode=ABORTED && echo "The wrapped script is not defined or not existing."

  # Put in start in Leetcode
  ${lockCommand} $_lock;
  echo "${RODDY_JOBID}:${startCode}:"`date +"%s"`":${TOOL_ID}" >> ${jobStateLogFile};
  ${unlockCommand} $_lock
  [[ ${startCode} == 60000 || ${startCode} == "ABORTED" ]] && echo "Exitting because a former job died." && exit 250

the job status is set to ABORTED, when the wrapped script is missing. Afterwards the wrong message is echoed: "Exitting because a former job died."

dankwart-de commented 6 years ago

This can be closed. We implemented checks for tool availability and accessibility. They will force Roddy to abort, when the tools don't exist or cannot be executed.

TheRoddyWMS / Roddy

If the compressed tool file exists and the extracted folder exists without files, Roddy runs will fail. #72