Changes between Version 8 and Version 9 of xQTLBioinformaticianScript

Timestamp:

2011-09-14T14:57:14+02:00 (13 years ago)

Author:

danny

Comment:

--

xQTLBioinformaticianScript

@@ -112 +112 @@
 * Run Plink system call inside R: `plink --noweb --file hapmap1 --assoc --out results`[[BR]]
 * Upload '''results.assoc''' back in database. (use servlet `/uploadfile`)
+
+
+=== User script for plink analysis ===
+
+{{{
+inputname <- getparameter("inputname",jobparams)
+  
+system(paste("wget ",paste(dbpath,"/downloadfile",sep=""),"?name=",inputname,"_ped -O ",inputname,".ped",sep=""))
+report(2,"PEDDownloaded")
+system(paste("wget ",paste(dbpath,"/downloadfile",sep=""),"?name=",inputname,"_map -O ",inputname,".map",sep=""))
+report(2,"MAPDownloaded")
+system(paste("plink --noweb --file ",inputname," --assoc --out ",outname,"",sep=""))
+report(2,"beforeUpload")
+postForm(paste(dbpath,"/uploadfile",sep=""),investigation_name='",investigationname,"', name='",outname,".assoc', type = 'InvestigationFile', file = fileUpload(filename='",outname,".assoc'), style='HTTPPOST')
+report(3,"PLINKfinished")
+}}}