scripts in ~ directory for starting: sh runAll.sh: to run Rserve, Solr and tomcat (execute runXXX.sh to run one of the three individually) sh checksError.sh: to check the running process, checks.log presented in home directory sh checkRun.sh: to check if the requried tools are running visit transmart by http://localhost:8080/transmart/
scripts in ~ directory for uploading: ./buildStudy.sh: generate the dataset folder in the studies/ , then please enter the position and manually edit the mapping file ./uploadClinical.sh: upload the study to transmart ./buildVCF.sh: generate the folder for vcf in studies/, will enter the folder if already exists ./uploadVCF.sh: upload the vcf file to transmart, please note that uploadClinical.sh must be executed before vcf is uploaded INSTRUCTIONS: After scp the files from cgdb, first buildStudy and modify MYSTUDY_column.txt and clinical.params, then uploadClinical. After clinical uplaoded, buildVCF and modify subject-sample-mapping file and vcf.params, then uploadVCF.
username and passwords the virtual machine: username = password = transmart postgresql: username = password = postgres (if necessary) transmart: username = password = admin
Directory explanation: in ~/transmart/transmart-data/samples: studies/ stores all the dataset files common/ stores the load scripts postgres/ stores the load scripts (as transmart is based on postgresql, oracle/ will not be involved)
Usually we will work in ~/transmart/transmart-data/ With the following commands in this directory, enter postgresql: . ./vars $PGSQL_BIN\psql postgres
TODO: more information in https://wiki.transmartfoundation.org/