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November 22, 2021 14:30
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| { | |
| "environment_variables": { | |
| "OBC_WORKFLOW_NAME": "my_fab_wf", | |
| "OBC_WORKFLOW_EDIT": "2", | |
| "OBC_NICE_ID": "my_fab_wf__2", | |
| "OBC_RANDOM_NICE_ID": "TSgb2", | |
| "OBC_SERVER": "http://0.0.0.0:8200/platform" | |
| }, | |
| "steps": { | |
| "INIT_STEP": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n\n\n\n\nif [ -n \"${OBC_WORK_PATH}\" ] ; then\n export OBC_REPORT_PATH=${OBC_WORK_PATH}/${OBC_NICE_ID}.html\n export OBC_REPORT_DIR=${OBC_WORK_PATH}/${OBC_NICE_ID}\n mkdir -p ${OBC_REPORT_DIR}\n echo \"OBC: Report filename: ${OBC_REPORT_PATH}\"\n\ncat > ${OBC_REPORT_PATH} << OBCENDOFFILE\n<!DOCTYPE html>\n<html lang=\"en\">\n <head>\n <meta http-equiv=\"Content-Type\" content=\"text/html; charset=utf-8\" />\n </head>\n <body>\n <p>\n OpenBio Server: <a href=\"${OBC_SERVER}\">${OBC_SERVER}</a> <br>\n Workflow: <a href=\"${OBC_SERVER}/w/${OBC_WORKFLOW_NAME}/${OBC_WORKFLOW_EDIT}\">${OBC_WORKFLOW_NAME}/${OBC_WORKFLOW_EDIT}</a> <br>\n\n <p>\n <h3>Intermediate Variables:</h3>\n <ul>\n <!-- {{INTERMEDIATE_VARIABLE}} -->\n </ul>\n\n <p>\n <h3>Output Variables:</h3>\n <ul>\n <!-- {{OUTPUT_VARIABLE}} -->\n </ul>\n\n </body>\n</html>\nOBCENDOFFILE\nfi\n\n\n\ncat > ${OBC_WORK_PATH}/obc_functions.sh << 'OBCENDOFFILE'\n\n\n\nexport OBC_REPORT_PATH=${OBC_WORK_PATH}/${OBC_NICE_ID}.html\nexport OBC_REPORT_DIR=${OBC_WORK_PATH}/${OBC_NICE_ID}\n\nfunction REPORT() {\n if [ -n \"${OBC_WORK_PATH}\" ] ; then\n local VAR=$1\n local TIMENOW=$(date)\n local WHOCALLEDME=$(caller 0 | awk '{print $2}')\n\n if [ -z $3 ] ; then\n local TAG=INTERMEDIATE_VARIABLE\n else\n local TAG=$3\n fi\n\n if [ ${TAG} == \"INTERMEDIATE_VARIABLE\" ] ; then\n local EXTRA=\"${TIMENOW}. Called from: ${WHOCALLEDME}\"\n else\n local EXTRA=\"\"\n fi\n\n local FILEKIND=$(file \"${2}\")\n # echo \"OBC: FILE RESULT ${FILEKIND}\"\n if [[ $FILEKIND == *\"PNG image data\"* ]]; then\n local NEWFILENAME=${OBC_REPORT_DIR}/$(basename ${2})\n local LOCALFILENAME=${OBC_NICE_ID}/$(basename ${2})\n cp ${2} ${NEWFILENAME}\n local HTML=\"<li>${EXTRA} ${VAR}: <br><img src=\\\"${LOCALFILENAME}\\\"></li>\\\\\\\\n <!-- {{${TAG}}} -->\\\\\\\\n\"\n elif [[ $FILEKIND == *\"PDF document\"* ]]; then\n local NEWFILENAME=${OBC_REPORT_DIR}/$(basename ${2})\n local LOCALFILENAME=${OBC_NICE_ID}/$(basename ${2})\n cp ${2} ${NEWFILENAME}\n local HTML=\"<li>${EXTRA} ${VAR}: <br><a href=\\\"${LOCALFILENAME}\\\">${LOCALFILENAME}</a></li>\\\\\\\\n <!-- {{${TAG}}} -->\\\\\\\\n\"\n else\n local VALUE=$(echo \"${2}\" | sed 's/&/\\\\\\&/g; s/</\\\\\\</g; s/>/\\\\\\>/g; s/\"/\\\\\\"/g; s/'\"'\"'/\\\\\\'/g')\n local HTML=\"<li>${EXTRA} ${VAR}=${VALUE}</li>\\\\\\\\n <!-- {{${TAG}}} -->\\\\\\\\n\"\n fi\n\n sed -i -e \"s|<\\!-- {{${TAG}}} -->|${HTML}|\" ${OBC_REPORT_PATH}\n sed 's/\\\\n/\\\n/g' ${OBC_REPORT_PATH} > ${OBC_REPORT_PATH}.tmp\n mv ${OBC_REPORT_PATH}.tmp ${OBC_REPORT_PATH}\n fi\n}\n\n\n\nOBCENDOFFILE\n\ntouch ${OBC_WORK_PATH}/TSgb2_inputs.sh\n", | |
| "run_after": [], | |
| "type": "initial" | |
| }, | |
| "wget__latest__1": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n### BASH INSTALLATION COMMANDS FOR TOOL: wget/latest/1\necho \"OBC: INSTALLING TOOL: wget/latest/1\"\n(\n:\n# Insert the BASH commands that install this tool\n# You can use these environment variables: \n# ${OBC_TOOL_PATH}: path to tools directory \n# ${OBC_DATA_PATH}: path to data directory\n\napt-get update\napt-get install -y wget \n)\necho \"OBC: INSTALLATION OF TOOL: wget/latest/1 . COMPLETED\"\n### END OF INSTALLATION COMMANDS FOR TOOL: wget/latest/1\n\n### BASH VALIDATION COMMANDS FOR TOOL: wget/latest/1\necho \"OBC: VALIDATING THE INSTALLATION OF THE TOOL: wget/latest/1\"\n(\n:\n# Insert the BASH commands that confirm that this tool is correctly installed\n# In success, this script should return 0 exit code.\n# A non-zero exit code, means failure to validate installation.\n\nwhich wget\n)\nif [ $? -eq 0 ] ; then\n echo \"OBC: VALIDATION FOR TOOL: wget/latest/1 SUCCEEDED\"\nelse\n echo \"OBC: VALIDATION FOR TOOL: wget/latest/1 FAILED\"\nfi\n\n### END OF VALIDATION COMMANDS FOR TOOL: wget/latest/1\n\n### SETTING TOOL VARIABLES FOR: wget/latest/1\nexport wget__latest__1__path=\"/usr/bin/wget\" # path to exec \necho \"OBC: SET wget__latest__1__path=\\\"$wget__latest__1__path\\\" <-- path to exec \"\n### END OF SETTING TOOL VARIABLES FOR: wget/latest/1\n\n### CREATING BASH WITH TOOL VARIABLES\ncat > ${OBC_WORK_PATH}/wget__latest__1_VARS.sh << ENDOFFILE\nwget__latest__1__path=\"/usr/bin/wget\"\nENDOFFILE\n", | |
| "run_after": [ | |
| "INIT_STEP" | |
| ], | |
| "type": "tool_installation" | |
| }, | |
| "unzip__latest__1": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n### BASH INSTALLATION COMMANDS FOR TOOL: unzip/latest/1\necho \"OBC: INSTALLING TOOL: unzip/latest/1\"\n### READING VARIABLES FROM ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n\n(\n:\n# Insert the BASH commands that install this tool\n# You can use these environment variables: \n# ${OBC_TOOL_PATH}: path to tools directory \n# ${OBC_DATA_PATH}: path to data directory\n\napt-get install -y unzip \n)\necho \"OBC: INSTALLATION OF TOOL: unzip/latest/1 . COMPLETED\"\n### END OF INSTALLATION COMMANDS FOR TOOL: unzip/latest/1\n\n### BASH VALIDATION COMMANDS FOR TOOL: unzip/latest/1\necho \"OBC: VALIDATING THE INSTALLATION OF THE TOOL: unzip/latest/1\"\n(\n:\n# Insert the BASH commands that confirm that this tool is correctly installed\n# In success, this script should return 0 exit code.\n# A non-zero exit code, means failure to validate installation.\n\nwhich unzip\n\n)\nif [ $? -eq 0 ] ; then\n echo \"OBC: VALIDATION FOR TOOL: unzip/latest/1 SUCCEEDED\"\nelse\n echo \"OBC: VALIDATION FOR TOOL: unzip/latest/1 FAILED\"\nfi\n\n### END OF VALIDATION COMMANDS FOR TOOL: unzip/latest/1\n\n### SETTING TOOL VARIABLES FOR: unzip/latest/1\nexport unzip__latest__1__path=\"/usr/bin/unzip\" # path to exec \necho \"OBC: SET unzip__latest__1__path=\\\"$unzip__latest__1__path\\\" <-- path to exec \"\n### END OF SETTING TOOL VARIABLES FOR: unzip/latest/1\n\n### CREATING BASH WITH TOOL VARIABLES\ncat > ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh << ENDOFFILE\nunzip__latest__1__path=\"/usr/bin/unzip\"\nENDOFFILE\n", | |
| "run_after": [ | |
| "INIT_STEP", | |
| "wget__latest__1" | |
| ], | |
| "type": "tool_installation" | |
| }, | |
| "python__3_8__1": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n### BASH INSTALLATION COMMANDS FOR TOOL: python/3.8/1\necho \"OBC: INSTALLING TOOL: python/3.8/1\"\n### READING VARIABLES FROM ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n\n### READING VARIABLES FROM ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n\n(\n:\n# Insert the BASH commands that install this tool\n# You can use these environment variables: \n# ${OBC_TOOL_PATH}: path to tools directory \n# ${OBC_DATA_PATH}: path to data directory\n\napt-get install -y python3.8\n)\necho \"OBC: INSTALLATION OF TOOL: python/3.8/1 . COMPLETED\"\n### END OF INSTALLATION COMMANDS FOR TOOL: python/3.8/1\n\n### BASH VALIDATION COMMANDS FOR TOOL: python/3.8/1\necho \"OBC: VALIDATING THE INSTALLATION OF THE TOOL: python/3.8/1\"\n(\n:\n# Insert the BASH commands that confirm that this tool is correctly installed\n# In success, this script should return 0 exit code.\n# A non-zero exit code, means failure to validate installation.\n\nwhich python3.8\n\n)\nif [ $? -eq 0 ] ; then\n echo \"OBC: VALIDATION FOR TOOL: python/3.8/1 SUCCEEDED\"\nelse\n echo \"OBC: VALIDATION FOR TOOL: python/3.8/1 FAILED\"\nfi\n\n### END OF VALIDATION COMMANDS FOR TOOL: python/3.8/1\n\n### SETTING TOOL VARIABLES FOR: python/3.8/1\nexport python__3_8__1__path=\"/usr/bin/python3.8\" # zxcvzxcv \necho \"OBC: SET python__3_8__1__path=\\\"$python__3_8__1__path\\\" <-- zxcvzxcv \"\n### END OF SETTING TOOL VARIABLES FOR: python/3.8/1\n\n### CREATING BASH WITH TOOL VARIABLES\ncat > ${OBC_WORK_PATH}/python__3_8__1_VARS.sh << ENDOFFILE\npython__3_8__1__path=\"/usr/bin/python3.8\"\nENDOFFILE\n", | |
| "run_after": [ | |
| "INIT_STEP", | |
| "wget__latest__1", | |
| "unzip__latest__1" | |
| ], | |
| "type": "tool_installation" | |
| }, | |
| "plink__1_07_x86_64__1": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n### BASH INSTALLATION COMMANDS FOR TOOL: plink/1.07_x86_64/1\necho \"OBC: INSTALLING TOOL: plink/1.07_x86_64/1\"\n### READING VARIABLES FROM ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n\n### READING VARIABLES FROM ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n\n### READING VARIABLES FROM ${OBC_WORK_PATH}/python__3_8__1_VARS.sh\n. ${OBC_WORK_PATH}/python__3_8__1_VARS.sh\n\n(\n:\n# Insert the BASH commands that install this tool\n# You can use these environment variables: \n# ${OBC_TOOL_PATH}: path to tools directory \n# ${OBC_DATA_PATH}: path to data directory\n\n${wget__latest__1__path} -O ${OBC_TOOL_PATH}/plink-1.07-x86_64.zip \"https://zzz.bwh.harvard.edu/plink/dist/plink-1.07-x86_64.zip\"\n\n${unzip__latest__1__path} ${OBC_TOOL_PATH}/plink-1.07-x86_64.zip -d ${OBC_TOOL_PATH}\n\n\n)\necho \"OBC: INSTALLATION OF TOOL: plink/1.07_x86_64/1 . COMPLETED\"\n### END OF INSTALLATION COMMANDS FOR TOOL: plink/1.07_x86_64/1\n\n### BASH VALIDATION COMMANDS FOR TOOL: plink/1.07_x86_64/1\necho \"OBC: VALIDATING THE INSTALLATION OF THE TOOL: plink/1.07_x86_64/1\"\n(\n:\n# Insert the BASH commands that confirm that this tool is correctly installed\n# In success, this script should return 0 exit code.\n# A non-zero exit code, means failure to validate installation.\n\n${OBC_TOOL_PATH}/plink-1.07-x86_64/plink --help\n\n)\nif [ $? -eq 0 ] ; then\n echo \"OBC: VALIDATION FOR TOOL: plink/1.07_x86_64/1 SUCCEEDED\"\nelse\n echo \"OBC: VALIDATION FOR TOOL: plink/1.07_x86_64/1 FAILED\"\nfi\n\n### END OF VALIDATION COMMANDS FOR TOOL: plink/1.07_x86_64/1\n\n### SETTING TOOL VARIABLES FOR: plink/1.07_x86_64/1\nexport plink__1_07_x86_64__1__path=\"${OBC_TOOL_PATH}/plink-1.07-x86_64/plink\" # path to exec \necho \"OBC: SET plink__1_07_x86_64__1__path=\\\"$plink__1_07_x86_64__1__path\\\" <-- path to exec \"\n### END OF SETTING TOOL VARIABLES FOR: plink/1.07_x86_64/1\n\n### CREATING BASH WITH TOOL VARIABLES\ncat > ${OBC_WORK_PATH}/plink__1_07_x86_64__1_VARS.sh << ENDOFFILE\nplink__1_07_x86_64__1__path=\"${OBC_TOOL_PATH}/plink-1.07-x86_64/plink\"\nENDOFFILE\n", | |
| "run_after": [ | |
| "INIT_STEP", | |
| "wget__latest__1", | |
| "unzip__latest__1", | |
| "python__3_8__1" | |
| ], | |
| "type": "tool_installation" | |
| }, | |
| "test_script__1__2": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n### BASH INSTALLATION COMMANDS FOR TOOL: test_script/1/2\necho \"OBC: INSTALLING TOOL: test_script/1/2\"\n### READING VARIABLES FROM ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n\n### READING VARIABLES FROM ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n\n### READING VARIABLES FROM ${OBC_WORK_PATH}/python__3_8__1_VARS.sh\n. ${OBC_WORK_PATH}/python__3_8__1_VARS.sh\n\n### READING VARIABLES FROM ${OBC_WORK_PATH}/plink__1_07_x86_64__1_VARS.sh\n. ${OBC_WORK_PATH}/plink__1_07_x86_64__1_VARS.sh\n\n(\n:\n# Insert the BASH commands that install this tool\n# You can use these environment variables: \n# ${OBC_TOOL_PATH}: path to tools directory \n# ${OBC_DATA_PATH}: path to data directory\n\ncat > ${OBC_TOOL_PATH}/script.py << EOF\nimport sys\n\ns = []\nwith open(sys.argv[1]) as f:\n \n f.readline()\n ls = f.readline().split()\n s.append(float(ls[4]))\n\nresult = sum(s)/len(s)\n\nwith open(sys.argv[2], 'w') as f:\n f.write(str(result) + '\\n')\n\nprint ('script OK')\n\nEOF\n)\necho \"OBC: INSTALLATION OF TOOL: test_script/1/2 . COMPLETED\"\n### END OF INSTALLATION COMMANDS FOR TOOL: test_script/1/2\n\n### BASH VALIDATION COMMANDS FOR TOOL: test_script/1/2\necho \"OBC: VALIDATING THE INSTALLATION OF THE TOOL: test_script/1/2\"\n(\n:\n# Insert the BASH commands that confirm that this tool is correctly installed\n# In success, this script should return 0 exit code.\n# A non-zero exit code, means failure to validate installation.\n\nexit 0\n\n)\nif [ $? -eq 0 ] ; then\n echo \"OBC: VALIDATION FOR TOOL: test_script/1/2 SUCCEEDED\"\nelse\n echo \"OBC: VALIDATION FOR TOOL: test_script/1/2 FAILED\"\nfi\n\n### END OF VALIDATION COMMANDS FOR TOOL: test_script/1/2\n\n### SETTING TOOL VARIABLES FOR: test_script/1/2\nexport test_script__1__2__path=\"${OBC_TOOL_PATH}/script.py\" # path to script \necho \"OBC: SET test_script__1__2__path=\\\"$test_script__1__2__path\\\" <-- path to script \"\n### END OF SETTING TOOL VARIABLES FOR: test_script/1/2\n\n### CREATING BASH WITH TOOL VARIABLES\ncat > ${OBC_WORK_PATH}/test_script__1__2_VARS.sh << ENDOFFILE\ntest_script__1__2__path=\"${OBC_TOOL_PATH}/script.py\"\nENDOFFILE\n", | |
| "run_after": [ | |
| "INIT_STEP", | |
| "wget__latest__1", | |
| "unzip__latest__1", | |
| "python__3_8__1", | |
| "plink__1_07_x86_64__1" | |
| ], | |
| "type": "tool_installation" | |
| }, | |
| "step__main_step__my_fab_wf__2__1": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n. ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/python__3_8__1_VARS.sh\n. ${OBC_WORK_PATH}/plink__1_07_x86_64__1_VARS.sh\n. ${OBC_WORK_PATH}/test_script__1__2_VARS.sh\n. ${OBC_WORK_PATH}/TSgb2_inputs.sh\n. ${OBC_WORK_PATH}/obc_functions.sh\nOBC_START=$(eval \"declare\")\n:\n# Insert the BASH commands for this step.\n# You can use the variable ${OBC_WORK_PATH} as your working directory.\n# Also read the Documentation about the REPORT and the PARALLEL commands.\n\nFN=TEST\n\n\nOBC_CURRENT=$(eval \"declare\")\ncomm -3 <(echo \"$OBC_START\" | grep -v \"_=\" | sort) <(echo \"$OBC_CURRENT\" | grep -v OBC_START | grep -v PIPESTATUS | grep -v \"_=\" | sort) > ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__1_VARS.sh\n", | |
| "run_after": [ | |
| "INIT_STEP", | |
| "wget__latest__1", | |
| "unzip__latest__1", | |
| "python__3_8__1", | |
| "plink__1_07_x86_64__1", | |
| "test_script__1__2" | |
| ], | |
| "type": "simple" | |
| }, | |
| "step__create_dataset__my_fab_wf__2__1": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n. ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/python__3_8__1_VARS.sh\n. ${OBC_WORK_PATH}/plink__1_07_x86_64__1_VARS.sh\n. ${OBC_WORK_PATH}/test_script__1__2_VARS.sh\n. ${OBC_WORK_PATH}/TSgb2_inputs.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__1_VARS.sh\n. ${OBC_WORK_PATH}/obc_functions.sh\nOBC_START=$(eval \"declare\")\n:\n# Insert the BASH commands for this step.\n# You can use the variable ${OBC_WORK_PATH} as your working directory.\n# Also read the Documentation about the REPORT and the PARALLEL commands.\n\nMAP=${OBC_WORK_PATH}/${FN}.map\nPED=${OBC_WORK_PATH}/${FN}.ped\n\ncat > ${MAP} << EOF\n1 snp1 0 1\n1 snp2 0 2\nEOF\n\ncat > ${PED} << EOF\n1 1 0 0 1 1 A A G T\n2 1 0 0 1 1 A C T G\n3 1 0 0 1 1 C C G G\n4 1 0 0 1 2 A C T T\n5 1 0 0 1 2 C C G T\n6 1 0 0 1 2 C C T T\nEOF\n\n\nOBC_CURRENT=$(eval \"declare\")\ncomm -3 <(echo \"$OBC_START\" | grep -v \"_=\" | sort) <(echo \"$OBC_CURRENT\" | grep -v OBC_START | grep -v PIPESTATUS | grep -v \"_=\" | sort) > ${OBC_WORK_PATH}/step__create_dataset__my_fab_wf__2__1_VARS.sh\n", | |
| "run_after": [ | |
| "INIT_STEP", | |
| "wget__latest__1", | |
| "unzip__latest__1", | |
| "python__3_8__1", | |
| "plink__1_07_x86_64__1", | |
| "test_script__1__2", | |
| "step__main_step__my_fab_wf__2__1" | |
| ], | |
| "type": "simple" | |
| }, | |
| "step__main_step__my_fab_wf__2__2": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n. ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/python__3_8__1_VARS.sh\n. ${OBC_WORK_PATH}/plink__1_07_x86_64__1_VARS.sh\n. ${OBC_WORK_PATH}/test_script__1__2_VARS.sh\n. ${OBC_WORK_PATH}/TSgb2_inputs.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__1_VARS.sh\n. ${OBC_WORK_PATH}/step__create_dataset__my_fab_wf__2__1_VARS.sh\n. ${OBC_WORK_PATH}/obc_functions.sh\nOBC_START=$(eval \"declare\")\n\n\n\nOBC_CURRENT=$(eval \"declare\")\ncomm -3 <(echo \"$OBC_START\" | grep -v \"_=\" | sort) <(echo \"$OBC_CURRENT\" | grep -v OBC_START | grep -v PIPESTATUS | grep -v \"_=\" | sort) > ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__2_VARS.sh\n", | |
| "run_after": [ | |
| "INIT_STEP", | |
| "wget__latest__1", | |
| "unzip__latest__1", | |
| "python__3_8__1", | |
| "plink__1_07_x86_64__1", | |
| "test_script__1__2", | |
| "step__main_step__my_fab_wf__2__1", | |
| "step__create_dataset__my_fab_wf__2__1" | |
| ], | |
| "type": "simple" | |
| }, | |
| "step__main_step__my_fab_wf__2__3": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n. ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/python__3_8__1_VARS.sh\n. ${OBC_WORK_PATH}/plink__1_07_x86_64__1_VARS.sh\n. ${OBC_WORK_PATH}/test_script__1__2_VARS.sh\n. ${OBC_WORK_PATH}/TSgb2_inputs.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__2_VARS.sh\n. ${OBC_WORK_PATH}/obc_functions.sh\nOBC_START=$(eval \"declare\")\n:\n\n${plink__1_07_x86_64__1__path} --noweb --file ${OBC_WORK_PATH}/${FN} --freq --out ${OBC_WORK_PATH}/freqs\n\nOBC_CURRENT=$(eval \"declare\")\ncomm -3 <(echo \"$OBC_START\" | grep -v \"_=\" | sort) <(echo \"$OBC_CURRENT\" | grep -v OBC_START | grep -v PIPESTATUS | grep -v \"_=\" | sort) > ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__3_VARS.sh\n", | |
| "run_after": [ | |
| "INIT_STEP", | |
| "wget__latest__1", | |
| "unzip__latest__1", | |
| "python__3_8__1", | |
| "plink__1_07_x86_64__1", | |
| "test_script__1__2", | |
| "step__main_step__my_fab_wf__2__2" | |
| ], | |
| "type": "tool_invocation", | |
| "tool_to_call": "plink__1_07_x86_64__1" | |
| }, | |
| "step__main_step__my_fab_wf__2__4": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n. ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/python__3_8__1_VARS.sh\n. ${OBC_WORK_PATH}/plink__1_07_x86_64__1_VARS.sh\n. ${OBC_WORK_PATH}/test_script__1__2_VARS.sh\n. ${OBC_WORK_PATH}/TSgb2_inputs.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__1_VARS.sh\n. ${OBC_WORK_PATH}/step__create_dataset__my_fab_wf__2__1_VARS.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__2_VARS.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__3_VARS.sh\n. ${OBC_WORK_PATH}/obc_functions.sh\nOBC_START=$(eval \"declare\")\n\n \nRESULT_FN=${OBC_WORK_PATH}/result.txt\n\n\nOBC_CURRENT=$(eval \"declare\")\ncomm -3 <(echo \"$OBC_START\" | grep -v \"_=\" | sort) <(echo \"$OBC_CURRENT\" | grep -v OBC_START | grep -v PIPESTATUS | grep -v \"_=\" | sort) > ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__4_VARS.sh\n", | |
| "run_after": [ | |
| "INIT_STEP", | |
| "wget__latest__1", | |
| "unzip__latest__1", | |
| "python__3_8__1", | |
| "plink__1_07_x86_64__1", | |
| "test_script__1__2", | |
| "step__main_step__my_fab_wf__2__1", | |
| "step__create_dataset__my_fab_wf__2__1", | |
| "step__main_step__my_fab_wf__2__2", | |
| "step__main_step__my_fab_wf__2__3" | |
| ], | |
| "type": "simple" | |
| }, | |
| "step__main_step__my_fab_wf__2__5": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n. ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/python__3_8__1_VARS.sh\n. ${OBC_WORK_PATH}/plink__1_07_x86_64__1_VARS.sh\n. ${OBC_WORK_PATH}/test_script__1__2_VARS.sh\n. ${OBC_WORK_PATH}/TSgb2_inputs.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__4_VARS.sh\n. ${OBC_WORK_PATH}/obc_functions.sh\nOBC_START=$(eval \"declare\")\n:\n\n${python__3_8__1__path} ${test_script__1__2__path} ${OBC_WORK_PATH}/freqs.frq ${RESULT_FN}\n\nOBC_CURRENT=$(eval \"declare\")\ncomm -3 <(echo \"$OBC_START\" | grep -v \"_=\" | sort) <(echo \"$OBC_CURRENT\" | grep -v OBC_START | grep -v PIPESTATUS | grep -v \"_=\" | sort) > ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__5_VARS.sh\n", | |
| "run_after": [ | |
| "INIT_STEP", | |
| "wget__latest__1", | |
| "unzip__latest__1", | |
| "python__3_8__1", | |
| "plink__1_07_x86_64__1", | |
| "test_script__1__2", | |
| "step__main_step__my_fab_wf__2__4" | |
| ], | |
| "type": "tool_invocation", | |
| "tool_to_call": "python__3_8__1" | |
| }, | |
| "step__main_step__my_fab_wf__2__6": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n. ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/python__3_8__1_VARS.sh\n. ${OBC_WORK_PATH}/plink__1_07_x86_64__1_VARS.sh\n. ${OBC_WORK_PATH}/test_script__1__2_VARS.sh\n. ${OBC_WORK_PATH}/TSgb2_inputs.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__1_VARS.sh\n. ${OBC_WORK_PATH}/step__create_dataset__my_fab_wf__2__1_VARS.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__2_VARS.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__3_VARS.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__4_VARS.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__5_VARS.sh\n. ${OBC_WORK_PATH}/obc_functions.sh\nOBC_START=$(eval \"declare\")\n\n\noutput__outp__my_fab_wf__2=$(<${RESULT_FN})\n\n\n\nOBC_CURRENT=$(eval \"declare\")\ncomm -3 <(echo \"$OBC_START\" | grep -v \"_=\" | sort) <(echo \"$OBC_CURRENT\" | grep -v OBC_START | grep -v PIPESTATUS | grep -v \"_=\" | sort) > ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__6_VARS.sh\n", | |
| "run_after": [ | |
| "INIT_STEP", | |
| "wget__latest__1", | |
| "unzip__latest__1", | |
| "python__3_8__1", | |
| "plink__1_07_x86_64__1", | |
| "test_script__1__2", | |
| "step__main_step__my_fab_wf__2__1", | |
| "step__create_dataset__my_fab_wf__2__1", | |
| "step__main_step__my_fab_wf__2__2", | |
| "step__main_step__my_fab_wf__2__3", | |
| "step__main_step__my_fab_wf__2__4", | |
| "step__main_step__my_fab_wf__2__5" | |
| ], | |
| "type": "simple" | |
| }, | |
| "FINAL_STEP": { | |
| "bash": "export OBC_WORKFLOW_NAME=my_fab_wf\nexport OBC_WORKFLOW_EDIT=2\nexport OBC_NICE_ID=TSgb2\nexport OBC_SERVER=http://0.0.0.0:8200/platform\n\n. ${OBC_WORK_PATH}/wget__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/unzip__latest__1_VARS.sh\n. ${OBC_WORK_PATH}/python__3_8__1_VARS.sh\n. ${OBC_WORK_PATH}/plink__1_07_x86_64__1_VARS.sh\n. ${OBC_WORK_PATH}/test_script__1__2_VARS.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__1_VARS.sh\n. ${OBC_WORK_PATH}/step__create_dataset__my_fab_wf__2__1_VARS.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__2_VARS.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__3_VARS.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__4_VARS.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__5_VARS.sh\n. ${OBC_WORK_PATH}/step__main_step__my_fab_wf__2__6_VARS.sh\n. ${OBC_WORK_PATH}/obc_functions.sh\nREPORT output__outp__my_fab_wf__2 ${output__outp__my_fab_wf__2} OUTPUT_VARIABLE \n\n\nOBC_REPORT_TGZ=${OBC_WORK_PATH}/${OBC_NICE_ID}.tgz\n\n#echo \"RUNNING: \"\n#echo \"tar zcf ${OBC_REPORT_TGZ} -C ${OBC_WORK_PATH} ${OBC_NICE_ID}.html ${OBC_NICE_ID}/\"\n\ntar zcf ${OBC_REPORT_TGZ} -C ${OBC_WORK_PATH} ${OBC_NICE_ID}.html ${OBC_NICE_ID}/\n\necho \"{\\\"output__outp__my_fab_wf__2\\\": \\\"${output__outp__my_fab_wf__2}\\\"}\"\n", | |
| "run_after": [ | |
| "INIT_STEP", | |
| "wget__latest__1", | |
| "unzip__latest__1", | |
| "python__3_8__1", | |
| "plink__1_07_x86_64__1", | |
| "test_script__1__2", | |
| "step__main_step__my_fab_wf__2__1", | |
| "step__create_dataset__my_fab_wf__2__1", | |
| "step__main_step__my_fab_wf__2__2", | |
| "step__main_step__my_fab_wf__2__3", | |
| "step__main_step__my_fab_wf__2__4", | |
| "step__main_step__my_fab_wf__2__5", | |
| "step__main_step__my_fab_wf__2__6" | |
| ], | |
| "type": "final" | |
| } | |
| }, | |
| "input_parameters": {}, | |
| "output_parameters": { | |
| "output__outp__my_fab_wf__2": { | |
| "description": "fabulous result", | |
| "belongto": { | |
| "name": "my_fab_wf", | |
| "edit": 2 | |
| } | |
| } | |
| }, | |
| "first_step": "step__main_step__my_fab_wf__2__1", | |
| "DAG": { | |
| "INIT_STEP": [], | |
| "wget__latest__1": [ | |
| "INIT_STEP" | |
| ], | |
| "unzip__latest__1": [ | |
| "wget__latest__1" | |
| ], | |
| "python__3_8__1": [ | |
| "unzip__latest__1" | |
| ], | |
| "plink__1_07_x86_64__1": [ | |
| "python__3_8__1" | |
| ], | |
| "test_script__1__2": [ | |
| "plink__1_07_x86_64__1" | |
| ], | |
| "step__main_step__my_fab_wf__2__1": [ | |
| "test_script__1__2" | |
| ], | |
| "step__create_dataset__my_fab_wf__2__1": [ | |
| "step__main_step__my_fab_wf__2__1" | |
| ], | |
| "step__main_step__my_fab_wf__2__2": [ | |
| "step__create_dataset__my_fab_wf__2__1" | |
| ], | |
| "step__main_step__my_fab_wf__2__3": [ | |
| "step__main_step__my_fab_wf__2__2" | |
| ], | |
| "step__main_step__my_fab_wf__2__4": [ | |
| "step__main_step__my_fab_wf__2__3" | |
| ], | |
| "step__main_step__my_fab_wf__2__5": [ | |
| "step__main_step__my_fab_wf__2__4" | |
| ], | |
| "step__main_step__my_fab_wf__2__6": [ | |
| "step__main_step__my_fab_wf__2__5" | |
| ], | |
| "FINAL_STEP": [ | |
| "step__main_step__my_fab_wf__2__6" | |
| ] | |
| }, | |
| "environments": { | |
| "0": { | |
| "unzip__latest__1": [ | |
| "wget__latest__1" | |
| ], | |
| "plink__1_07_x86_64__1": [ | |
| "wget__latest__1", | |
| "unzip__latest__1" | |
| ], | |
| "wget__latest__1": [] | |
| }, | |
| "1": { | |
| "python__3_8__1": [], | |
| "test_script__1__2": [ | |
| "python__3_8__1" | |
| ] | |
| } | |
| } | |
| } | |
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