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A web based analysis viewer
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README.md

README

ECDP can be build and deployed on tomcat+mysql or you grab the docker version

for Docker: docker pull zackramjan/ecdp to start docker container: docker run -ti -d --privileged --name=ecdp_docker -v /sys/fs/cgroup:/sys/fs/cgroup:ro -p 8080:8080 ecdp (optionally you can add -p 3306:3306 if you want to connect to mariaDB/mysql)

to build: GXT4.0 GWT1.7 Java7 MariaDB

checkout, Gwt-compile, then deploy war dir to tomcat. make sure /ecdp/src/config.properties has your correct DB connection info.

to submit updates, use the following json syntax and post to addanalysis.jsp. note the the first 3 properties should be unique, but are not supplied by the system. you can use your internal LIMS ids or generate uuids if needed.

you can optionally include a file url for each metric, or if you just wish to associate files, you can skip metricName/Value for a given entry

{ "experimentID":"myExp564", "sampleId":"ABC23", "analysisID":"Run2_For_ABC455", "metrics":[ { "metricName":"Date_Sequenced", "metricValue":"Jan 22 2016"
}, { "metricName":"project", "metricValue":"ABC project", "metricFileName":"http://path-an-file.bam", "metricFileSize":123123 }, { "metricName":"sample_name", "metricValue":"zacktest" }, { "metricFileName":"s3://asdasd.asdad/123123.bam", "metricFileSize":123123 }, { "metricName":"processing", "metricValue":"nomeseq" } ] }

save your json to a file (ex: test.json) and upload to the server with curl: curl -H "Content-Type: application/json" -X POST -d @test.json http://www.ecdp.org/addanalysis.jsp

changes are initially stored in an intermediate table, to push to the main table for diplsay on the web: curl http://www.ecdp.org/updatedb.jsp

to delete an analysis curl --data "analysis_id=Run2_For_ABC455" http://www.ecdp.org/deleteanalysis.jsp

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