{"id":6380,"date":"2020-09-29T10:13:46","date_gmt":"2020-09-29T08:13:46","guid":{"rendered":"https:\/\/myoceane.fr\/?p=6380"},"modified":"2020-10-14T10:28:00","modified_gmt":"2020-10-14T08:28:00","slug":"bioi-cromwell-%e5%ad%b8%e7%bf%92%e7%b4%80%e9%8c%84","status":"publish","type":"post","link":"https:\/\/myoceane.fr\/index.php\/bioi-cromwell-%e5%ad%b8%e7%bf%92%e7%b4%80%e9%8c%84\/","title":{"rendered":"[BioI] Cromwell \u5b78\u7fd2\u7d00\u9304"},"content":{"rendered":"<div id=\"fb-root\"><\/div>\n<p style=\"text-align: justify;\">Cromwell \u662f\u4e00\u500b\u7528\u4f86\u57f7\u884c\u5de5\u4f5c\u6d41\u6558\u8ff0\u8a9e\u8a00 WDL (workflow description language) \u7684\u5e73\u53f0\uff0c\u4ed6\u662f\u7531 Broad Institute \u958b\u767c\u7684\u4e00\u500b\u958b\u6e90\u5c08\u6848\uff0cCromwell \u6bd4\u8f03\u53b2\u5bb3\u7684\u5730\u65b9\u662f\u53ef\u4ee5\u5229\u7528\u4e0d\u540c\u7684\u96f2\u5e73\u53f0\u7576\u4f5c\u4ed6\u7684\u5f8c\u53f0\u4f86\u8dd1 WDL \u7684\u5de5\u4f5c\u6d41\u8173\u672c\uff0c\u4f8b\u5982\u4e9e\u99ac\u905c\u7684 AWS \u6216\u662f Google Cloud\uff0c\u4ee5\u4e0b\u63d0\u4f9b\u4e00\u500b AWS \u4ecb\u7d39 Cromwell \u7684\u5f71\u7247\uff0c\u672c\u7bc7\u60f3\u8981\u7c21\u55ae\u8a18\u9304\u4e00\u4e9b\u6709\u95dc Cromwell \u7684\u57fa\u672c\u77e5\u8b58\u3002<\/p>\n\n\n<figure class=\"wp-block-embed-youtube wp-block-embed is-type-video is-provider-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"An Introduction to Running Cromwell on Amazon Web Services\" width=\"910\" height=\"512\" src=\"https:\/\/www.youtube.com\/embed\/TNQLRxw7ExY?start=1083&#038;feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n<p>\u95dc\u65bc Cromwell \u7684\u5c08\u6848\u53ef\u4ee5\u5728 <a href=\"https:\/\/github.com\/broadinstitute\/cromwell\">Github \u88e1\u9762<\/a>\u770b\u5230\uff0c\u4e0b\u8f09 cromwell \u5c08\u6848\u4e4b\u5f8c\u53ef\u4ee5\u8dd1&nbsp;<\/p>\n<pre class=\"lang:bash\">git clone https:\/\/github.com\/broadinstitute\/cromwell.git\ncd cromwell\nsbt assembly<\/pre>\n<p>\u5c31\u53ef\u4ee5\u5229\u7528 SBT (Simple Build Tool) \u53bb\u7de8\u8b6f\u4e26\u4e14\u6253\u5305 Cromwell\uff0c\u7406\u8ad6\u4e0a\u6210\u529f\u8dd1\u5b8c\uff0c\u4ee5\u4e0a\u7684 cmd \u53ef\u4ee5\u5f97\u5230\u4e00\u500b server \u7684 jar \u6a94\uff0c\u5982\u4e0b\u5716\u6240\u793a\uff1a<\/p>\n<pre class=\"lang:bash\">user:scala-2.12 user$ ls -l\ntotal 458768\ndrwxr-xr-x  6 user  staff        192  9 24 10:15 classes\n-rw-r--r--  1 user  staff  234582613  9 24 10:17 cromwell-54-a3242c6-SNAP.jar\ndrwxr-xr-x  3 user  staff         96  9 24 10:11 resource_managed<\/pre>\n<p>\u5099\u8a3b\uff1a\u5982\u679c\u662f\u8981\u6e05\u9664\u5df2\u7d93\u751f\u6210\u7684 jar \u6a94\uff0c\u56e0\u70ba\u6703\u4e00\u76f4\u7d2f\u7a4d\uff0c\u53ef\u4ee5\u4f7f\u7528<\/p>\n<pre class=\"lang:bash\">sbt clean cleanFiles<\/pre>\n<h4>\u555f\u52d5 Cromwell Swagger API<\/h4>\n<p>\u7576\u6709\u4e86 cromwell-XXX.jar\uff0c\u6b64\u6642\u53ef\u4ee5\u5229\u7528\u4ee5\u4e0b\u6307\u4ee4\u555f\u52d5 Cromwell Swagger\u3002<\/p>\n<pre class=\"lang:bash\">java -Dwebservice.port=8080 \n     -jar cromwell-54-a3242c6-SNAP.jar \n     server<\/pre>\n<p>log \u6a94\uff1a<\/p>\n<pre class=\"lang:bash\">2020-09-24 10:59:07,981  INFO  - Running with database db.url = jdbc:hsqldb:mem:cfaf72e7-f82e-4703-a693-6d46fb6760ef;shutdown=false;hsqldb.tx=mvcc\n2020-09-24 10:59:14,934  INFO  - Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000\n2020-09-24 10:59:14,945  INFO  - [RenameWorkflowOptionsInMetadata] 100%\n2020-09-24 10:59:15,037  INFO  - Running with database db.url = jdbc:hsqldb:mem:4c88b2a2-928a-47da-84bb-0caed4b5b91b;shutdown=false;hsqldb.tx=mvcc\n2020-09-24 10:59:15,455  INFO  - Slf4jLogger started\n2020-09-24 10:59:15,727 cromwell-system-akka.dispatchers.engine-dispatcher-6 INFO  - Workflow heartbeat configuration:\n{\n  \"cromwellId\" : \"cromid-3543c76\",\n  \"heartbeatInterval\" : \"2 minutes\",\n  \"ttl\" : \"10 minutes\",\n  \"failureShutdownDuration\" : \"5 minutes\",\n  \"writeBatchSize\" : 10000,\n  \"writeThreshold\" : 10000\n}\n2020-09-24 10:59:15,774 cromwell-system-akka.dispatchers.service-dispatcher-12 INFO  - Metadata summary refreshing every 1 second.\n2020-09-24 10:59:15,784 cromwell-system-akka.actor.default-dispatcher-13 INFO  - KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.\n2020-09-24 10:59:15,784 cromwell-system-akka.dispatchers.service-dispatcher-8 INFO  - WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.\n2020-09-24 10:59:15,789 cromwell-system-akka.dispatchers.engine-dispatcher-30 INFO  - JobStoreWriterActor configured to flush with batch size 1000 and process rate 1 second.\n2020-09-24 10:59:15,800 cromwell-system-akka.dispatchers.engine-dispatcher-30 INFO  - CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.\n2020-09-24 10:59:15,800  WARN  - 'docker.hash-lookup.gcr-api-queries-per-100-seconds' is being deprecated, use 'docker.hash-lookup.gcr.throttle' instead (see reference.conf)\n2020-09-24 10:59:16,090 cromwell-system-akka.dispatchers.engine-dispatcher-30 INFO  - JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.\n2020-09-24 10:59:16,999 cromwell-system-akka.dispatchers.engine-dispatcher-6 INFO  - Cromwell 54-a3242c6-SNAP service started on 0:0:0:0:0:0:0:0:8080...\n2020-09-24 10:59:21,106 cromwell-system-akka.dispatchers.engine-dispatcher-15 INFO  - Not triggering log of token queue status. Effective log interval = None<\/pre>\n<p><\/p>\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"565\" src=\"https:\/\/myoceane.fr\/wp-content\/uploads\/2020\/09\/\u622a\u5716-2020-09-24-\u4e0a\u534811.07.05-1024x565.png\" alt=\"\" class=\"wp-image-6392\" srcset=\"https:\/\/myoceane.fr\/wp-content\/uploads\/2020\/09\/\u622a\u5716-2020-09-24-\u4e0a\u534811.07.05-1024x565.png 1024w, https:\/\/myoceane.fr\/wp-content\/uploads\/2020\/09\/\u622a\u5716-2020-09-24-\u4e0a\u534811.07.05-300x165.png 300w, https:\/\/myoceane.fr\/wp-content\/uploads\/2020\/09\/\u622a\u5716-2020-09-24-\u4e0a\u534811.07.05-768x423.png 768w, https:\/\/myoceane.fr\/wp-content\/uploads\/2020\/09\/\u622a\u5716-2020-09-24-\u4e0a\u534811.07.05-1536x847.png 1536w, https:\/\/myoceane.fr\/wp-content\/uploads\/2020\/09\/\u622a\u5716-2020-09-24-\u4e0a\u534811.07.05-2048x1129.png 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption>\u555f\u52d5\u4e4b\u5f8c Cromwell Server REST API \u7684\u756b\u9762<\/figcaption><\/figure>\n\n\n<h5>\u76f4\u63a5\u57f7\u884c WDL (Workflow Description Language)<\/h5>\n<p>\u6211\u5011\u4e5f\u53ef\u4ee5\u76f4\u63a5\u900f\u904e jar \u6a94\u53bb\u57f7\u884c\u4e00\u500b wdl \u8173\u672c\uff0c\u9019\u908a\u53ef\u4ee5\u914d\u5408\u4e0d\u540c\u7684\u96f2\u5e73\u53f0\u4f86\u63a8\u9001 workflow \u7684\u5de5\u4f5c\uff01<\/p>\n<pre class=\"lang:bash\">java -Dconfig.file=~\/cromwell\/cromwell.example.backends\/AWS.conf \n     -jar cromwell-54-1637396-SNAP.jar \n     run ~\/cromwell_wdl\/hello_aws.wdl<\/pre>\n<p>\u5099\u8a3b\uff1a\u4ee5\u4e0a\u662f AWS \u7684\u7bc4\u4f8b\u3002<\/p>\n<h5>\u4f7f\u7528 Curl \u63a8\u9001 Wdl \u6a94\u6848<\/h5>\n<p style=\"text-align: justify;\">\u4e0a\u9762\u63d0\u4f9b REST API Swagger \u7684\u4ecb\u9762\uff0c\u7528\u6236\u9664\u4e86\u53ef\u4ee5\u5229\u7528\u7db2\u9801\u7684\u4ecb\u9762\u63a8\u9001\u5de5\u4f5c\u6d41\u4e4b\u5916\uff0c\u4e5f\u53ef\u4ee5\u5229\u7528 curl \u7684\u6307\u4ee4\u53bb\u63a8\u9001 HTTP \u7684\u5de5\u4f5c\uff0c\u4ee5\u4e0b\u63d0\u4f9b\u4e00\u500b curl \u7684\u7bc4\u4f8b\uff0c\u9664\u6b64\u4e4b\u5916\u4e5f\u53ef\u4ee5\u5728 swagger \u4ecb\u9762\u53d6\u5f97\u76f8\u5c0d\u61c9\u7684\u6307\u4ee4\u7d30\u7bc0\uff0c<a href=\"https:\/\/cromwell.readthedocs.io\/en\/stable\/tutorials\/TimingDiagrams\/#submit-to-cromwell\">\u5b98\u7db2\u7684\u4ecb\u7d39<\/a>\u3002<\/p>\n<pre class=\"lang:bash\">curl -X POST --header \"Accept: application\/json\"\\\n    -v \"localhost:8080\/api\/workflows\/v1\" \\\n    -F workflowSource=@aws.wdl \\\n    -F workflowInputs=@aws.inputs<\/pre>\n<p>\u5099\u8a3b\uff1a\u5f9e Swagger \u53d6\u5f97\u76f8\u5c0d\u61c9 curl \u65b9\u6cd5\u7684\u622a\u5716\u3002<\/p>\n\n\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"293\" src=\"https:\/\/myoceane.fr\/wp-content\/uploads\/2020\/10\/\u622a\u5716-2020-10-14-\u4e0a\u534810.05.31-1024x293.png\" alt=\"\" class=\"wp-image-6482\" srcset=\"https:\/\/myoceane.fr\/wp-content\/uploads\/2020\/10\/\u622a\u5716-2020-10-14-\u4e0a\u534810.05.31-1024x293.png 1024w, https:\/\/myoceane.fr\/wp-content\/uploads\/2020\/10\/\u622a\u5716-2020-10-14-\u4e0a\u534810.05.31-300x86.png 300w, https:\/\/myoceane.fr\/wp-content\/uploads\/2020\/10\/\u622a\u5716-2020-10-14-\u4e0a\u534810.05.31-768x219.png 768w, https:\/\/myoceane.fr\/wp-content\/uploads\/2020\/10\/\u622a\u5716-2020-10-14-\u4e0a\u534810.05.31-1536x439.png 1536w, https:\/\/myoceane.fr\/wp-content\/uploads\/2020\/10\/\u622a\u5716-2020-10-14-\u4e0a\u534810.05.31-2048x585.png 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>Cromwell \u662f\u4e00\u500b\u7528\u4f86\u57f7\u884c\u5de5\u4f5c\u6d41\u6558\u8ff0\u8a9e\u8a00 WDL (workflow description language) \u7684\u5e73\u53f0\uff0c\u4ed6\u662f\u7531 Broad Institute \u958b\u767c\u7684\u4e00\u500b\u958b\u6e90\u5c08\u6848\uff0cCromwell \u6bd4\u8f03\u53b2\u5bb3\u7684\u5730\u65b9\u662f\u53ef\u4ee5\u5229\u7528\u4e0d\u540c\u7684\u96f2\u5e73\u53f0\u7576\u4f5c\u4ed6\u7684\u5f8c\u53f0\u4f86\u8dd1 WDL \u7684\u5de5\u4f5c\u6d41\u8173\u672c\uff0c\u4f8b\u5982\u4e9e\u99ac\u905c\u7684 AWS \u6216\u662f Google Cloud\uff0c\u4ee5\u4e0b\u63d0\u4f9b\u4e00\u500b AWS \u4ecb\u7d39 Cromwell \u7684\u5f71\u7247\uff0c\u672c\u7bc7\u60f3\u8981\u7c21\u55ae\u8a18\u9304\u4e00\u4e9b\u6709\u95dc Cromwell \u7684\u57fa\u672c\u77e5\u8b58\u3002<\/p>\n","protected":false},"author":1,"featured_media":6444,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[337,14],"tags":[956],"class_list":["post-6380","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-bioinformatics","category-it-technology","tag-cromwell"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v24.6 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>[BioI] Cromwell \u5b78\u7fd2\u7d00\u9304 - \u60f3\u65b9\u6d89\u6cd5 - \u91cf\u74f6\u5916\u7684\u5929\u7a7a M-Y-Oceane<\/title>\n<meta name=\"description\" content=\"Cromwell \u662f\u4e00\u500b\u5de5\u4f5c\u6d41\u6558\u8ff0\u8a9e\u8a00 WDL (workflow description language) \u7684\u57f7\u884c\u5e73\u53f0\uff0c\u4ed6\u662f\u7531 Broad Institute \u958b\u767c\u7684\u4e00\u500b\u958b\u6e90\u5c08\u6848\uff0cCromwell \u6bd4\u8f03\u53b2\u5bb3\u7684\u5730\u65b9\u662f\u53ef\u4ee5\u5229\u7528\u4e0d\u540c\u7684\u96f2\u5e73\u53f0\u7576\u4f5c\u4ed6\u7684\u5f8c\u53f0\u4f86\u8dd1 WDL \u7684\u5de5\u4f5c\u6d41\u8173\u672c\uff0c\u4f8b\u5982\u4e9e\u99ac\u905c\u7684 AWS \u6216\u662f Google Cloud\uff0c\u4ee5\u4e0b\u63d0\u4f9b\u4e00\u500b AWS \u4ecb\u7d39 Cromwell \u7684\u5f71\u7247\uff0c\u672c\u7bc7\u60f3\u8981\u7c21\u55ae\u8a18\u9304\u4e00\u4e9b\u6709\u95dc Cromwell \u7684\u57fa\u672c\u77e5\u8b58\u3002\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/myoceane.fr\/index.php\/bioi-cromwell-\u5b78\u7fd2\u7d00\u9304\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"[BioI] Cromwell \u5b78\u7fd2\u7d00\u9304 - 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