| | 19 | = All our standard operation procedures = |
| | 20 | [[TOC()]] |
| | 21 | |
| | 22 | See MolgenisAppStories for requirements. |
| | 23 | |
| | 24 | == Molgenis Apps deployment SOPs == |
| | 25 | |
| | 26 | Stories that hold for any 'app': |
| | 27 | |
| | 28 | * [wiki:MolgenisServers] - listing of MOLGENIS servers |
| | 29 | * [http://www.molgenis.org/wiki/SopInstallationTomcat7#SopInstallationTomcat7 How to deploy Tomcat7] |
| | 30 | * [http://www.molgenis.org/wiki/SopInstallationDeployServerInHudson#SopInstallationDeployServerInHudson Deploy server in Hudson] |
| | 31 | * [wiki:SopCreateMolgenisVM Create Molgenis VM] - How to request and configure a new copy of 'molgenis gold' |
| | 32 | * [wiki:SopDeployMolgenisApps] - how to automatically check-out, build and run one of the molgenis_apps |
| | 33 | * [wiki:SopMolgenis] - how to check out and build a molgenis app |
| | 34 | * [wiki:SopLoadData] - how to load data into your app install |
| | 35 | * [wiki:SopUseJQuerytree] - how to find, instantiate and use |
| | 36 | * [wiki:SopGenericImporter] - how to use, how to import, how the interface works |
| | 37 | * [wiki:SopNightlyBuild] - how to create a nightly build |
| | 38 | * [wiki:SopUseGenericImporter] - how to use GenericImporter |
| | 39 | * [wiki:SopUpdateBbmriApp] - How to Update Bbmri App |
| | 40 | * [wiki:MysqlSetup Mysql setup] |
| | 41 | * [SopPrintScrum How to print the scrum cards] |
| | 42 | * [omxManual Omx manual] |
| | 43 | |
| | 44 | == Using the GCC compute cluster == |
| | 45 | |
| | 46 | * [wiki:SopUseGccCluster SOP Users] - How to use the GCC cluster |
| | 47 | * [wiki:GccSopNewUser SOP New User] - Creating a new user account for the GCC infrastructure |
| | 48 | * [wiki:GccCluster SOP Admins] - Configuration details of the GCC cluster |
| | 49 | |
| | 50 | == LifeLines Research portal deployment SOPs == |
| | 51 | Depends on above. Specific stories for LifeLines data: |
| | 52 | |
| | 53 | * SopConvertLifeLinesGenoData - how to prepare the geno data from release 3 + imputation (2 sets) |
| | 54 | * SopConvertLifeLinesPhenoData - how to load the database release |
| | 55 | * SopLinkVmToWom - how to link the virtual machine to the WOA |
| | 56 | * GccLifeLinesSopDeployPortal - how to deploy the Research Portal on a VM |
| | 57 | |
| | 58 | == LifeLines user manuals == |
| | 59 | * HelpUsingMatrix - How to select Measurements and filter matrix |
| | 60 | * HelpDownloadPlink - How to download PLINK ready files (TFAM, TPED) |
| | 61 | |
| | 62 | == !TupleTable SOPs == |
| | 63 | Depends on above. Specific stories for LifeLines data: |
| | 64 | |
| | 65 | * [http://www.molgenis.org/wiki/GccTupleTable JQGridPluginProtocol] - how to use the Tuple Table viewer |
| | 66 | |
| | 67 | == MOLGENIS/compute SOPs == |
| | 68 | |
| | 69 | * DeployDependencies - How to deploy tools and resources for your workflows on different backends (Grid, PBS cluster, etc.) |
