{"action":"created","issue":{"url":"https://api.github.com/repos/CellProfiler/CellProfiler/issues/1397","labels_url":"https://api.github.com/repos/CellProfiler/CellProfiler/issues/1397/labels{/name}","comments_url":"https://api.github.com/repos/CellProfiler/CellProfiler/issues/1397/comments","events_url":"https://api.github.com/repos/CellProfiler/CellProfiler/issues/1397/events","html_url":"https://github.com/CellProfiler/CellProfiler/issues/1397","id":92643791,"number":1397,"title":"export to spreadsheet in batch mode with -o option","user":{"login":"erexhepa","id":3286025,"avatar_url":"https://avatars.githubusercontent.com/u/3286025?v=3","gravatar_id":"","url":"https://api.github.com/users/erexhepa","html_url":"https://github.com/erexhepa","followers_url":"https://api.github.com/users/erexhepa/followers","following_url":"https://api.github.com/users/erexhepa/following{/other_user}","gists_url":"https://api.github.com/users/erexhepa/gists{/gist_id}","starred_url":"https://api.github.com/users/erexhepa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/erexhepa/subscriptions","organizations_url":"https://api.github.com/users/erexhepa/orgs","repos_url":"https://api.github.com/users/erexhepa/repos","events_url":"https://api.github.com/users/erexhepa/events{/privacy}","received_events_url":"https://api.github.com/users/erexhepa/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":2,"created_at":"2015-07-02T13:54:23Z","updated_at":"2015-07-03T08:31:33Z","closed_at":null,"body":"Hi,\r\n\r\nI'm running in the cluster in batch mode using by using the create batch files module. To send jobs to different nodes of the cluster I'm using the -f and -l switch but to generate the output for each run I use -o switch by giving a folder name. \r\n\r\nEverything goes smoothly during the analysis and there are folders created by each job but folders are empty. \r\n\r\nHere is an example of a command send to to one of the nodes.\r\n\r\npython /users/biocomp/rexhepaj/CP_Bioclust/CellProfiler/CellProfiler.py -c -r -p testBatchmode/Batch_data.h5 -f 2 -l 2 -o testFolder\r\n\r\nI was wondering if there is patch for this or if I'm doing something wrong with the options given to the command line to set the DOF for each job.\r\n\r\nThanks\r\nElton"},"comment":{"url":"https://api.github.com/repos/CellProfiler/CellProfiler/issues/comments/118274747","html_url":"https://github.com/CellProfiler/CellProfiler/issues/1397#issuecomment-118274747","issue_url":"https://api.github.com/repos/CellProfiler/CellProfiler/issues/1397","id":118274747,"user":{"login":"erexhepa","id":3286025,"avatar_url":"https://avatars.githubusercontent.com/u/3286025?v=3","gravatar_id":"","url":"https://api.github.com/users/erexhepa","html_url":"https://github.com/erexhepa","followers_url":"https://api.github.com/users/erexhepa/followers","following_url":"https://api.github.com/users/erexhepa/following{/other_user}","gists_url":"https://api.github.com/users/erexhepa/gists{/gist_id}","starred_url":"https://api.github.com/users/erexhepa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/erexhepa/subscriptions","organizations_url":"https://api.github.com/users/erexhepa/orgs","repos_url":"https://api.github.com/users/erexhepa/repos","events_url":"https://api.github.com/users/erexhepa/events{/privacy}","received_events_url":"https://api.github.com/users/erexhepa/received_events","type":"User","site_admin":false},"created_at":"2015-07-03T08:31:33Z","updated_at":"2015-07-03T08:31:33Z","body":"I'm using version 2.1.1. \r\n\r\nI saw the patch you metioned above and tried it but had an error afterwards when starting the main script of cell profiler. It seemed to be due to the JVM. Anyway I will give another shot to the patch above because I had applied several patches before the \r\nhttps://github.com/CellProfiler/CellProfiler/commit/3fdcb3216a1913e1dc7934de719b0f2d804d7e3c and now since then I did a fresh install. \r\n\r\nThanks "}}