| 5 | | go to 'Run QTL mapping' |
| | 5 | Start by clicking ''Run QTL mapping'' in the main menu. This will take you to the central screen for starting new or monitoring existing 'jobs', in this case QTL mapping. |
| | 6 | |
| | 7 | === Starting a new job === |
| | 8 | |
| | 9 | * Click ''Create new job'' after selecting the compute location. ''Local'' means starting it on the same computer where the application is currently running. ''Cluster'' means submitting it to a remote location where more computational power might be available. |
| | 10 | |
| | 11 | Step 1 |
| | 12 | * Give a name to the output data matrix. If it happens to exist, a timestamp will be added to make it unique. |
| | 13 | * Select the kind of analysis you would like to run, e.g. ''Rqtl_analysis''. |
| | 14 | * Select the amount of subjobs this computational task should be divided into. For larger sets of traits, it is beneficial to set this to higher value, so many jobs will run in parallel. However, if little power (CPUs) is available, a high setting may actually slow the task down. If you are in doubt, use the default of 5. |
| | 15 | |
| | 16 | Step 2: |
| | 17 | * Select the datasets to use for this analysis. When many datasets are uploaded and tagged as pheno- and genotype data, be careful to select the right combination. |
| | 18 | * Select the parameters you would like to use. |
| | 19 | * Start the analysis by pressing ''Start'', this will take you to the job manager where you can follow its progress. |
| | 20 | |
| | 21 | Note that if you cannot find back your dataset, or are unhappy with any of the parameters, a bioinformatician (or admin) can configure them for you. |
| 20 | | * Use to the 'Compute on data' button in the welcome screen or select 'Start and manage jobs' from the main menu |
| 21 | | * Click the 'Job manager' button, this will take you to the job manager interface |
| 22 | | * The Refresh box can be used to speed up / slow down polling interval (5, 15, 30, 60 seconds or off) |
| 23 | | |
| 24 | | === Analysis administration === |
| 25 | | |
| 26 | | Go to the Job manager here the following administration task can be performed: |
| 27 | | |
| 28 | | * Status of all running sub jobs can be monitored by hovering over the sub job box |
| 29 | | * Provenance is kept by storing the analysis parameters in the database these can be viewed by hovering over the hover button |
| 30 | | * Provenance of completed jobs can be removed by clicking the [x] button, NOTE: this will NOT delete results stored into the database |
| 31 | | * Failed sub jobs (status -1) can be resubmitted by clicking on them |
| 32 | | |
| 33 | | In the 'Browse data' section: |
| 34 | | |
| 35 | | * Raw numeric output can be viewed / edited / deleted from each analysis (Type: Data) |
| 36 | | * Data consistency checks can be seen in the Inspector tab (Type: Data, Sub Types: Inspector) |
| 37 | | * Basic plots can be created / viewed 'on the fly' (Type: Data, Sub Types: Heatmap / Rplot) |
| 38 | | * Image data can be viewed / edited / deleted from each analysis (Type: Image) |
| | 25 | * In the ''Run QTL mapping'' screen, click on ''Go to job manager''. This will take you to the job manager. |
| | 26 | * The status of all running subjobs can be seen here. The color coding indicates the status. Failed is red/-1, submitted orange/0, queued yellow/1, running blue/2, completed green/3. |
| | 27 | * Provenance is kept by storing all analysis parameters in the database. This can be viewed by holding your mouse cursor over the text marked as ''hover''. |
| | 28 | * Provenance of completed jobs can be removed by clicking the delete button marked as [x]. Note that this will not delete results already stored in the database. |
| | 29 | * Failed sub jobs (statuscode -1) can be resubmitted by clicking on them. |
| | 30 | * Note that you must have supplied your remote login credentials for resubmission of cluster jobs. (Needs a fix: currently this can only be done by submitting a new job) |
| | 31 | * The ''refresh page'' box can be used to speed up or slow down the polling interval. (5, 15, 30, 60 seconds or off) |
