Anduril User Guide February 27, 2015 Kristian Ovaska Ping Chen Marko Laakso Ville Rantanen Riku Louhimo Sirkku Karinen Javier Nu´nez˜ Fontarnau Vladimir Rogojin Roman Sirokov Contact:
[email protected] Biomedicum Helsinki, Finland Contents I Anduril for End Users1 1 Introduction to Anduril1 1.1 Component model............................2 1.1.1 Type parameters........................4 1.1.2 Resource bundles........................4 1.2 Workflows................................4 1.2.1 Composite components.....................5 1.2.2 Conditional branches......................5 1.3 Workflow execution...........................6 1.4 Component and workflow quality control................7 2 Installation and requirements9 2.1 VirtualBox image installation......................9 2.2 Debian package installation....................... 13 2.3 Binary package installation....................... 13 3 Using Anduril 16 3.1 Eclipse interface............................. 16 3.1.1 Eclipse plugin installation................... 16 3.1.2 Configuring the plugin...................... 17 3.1.3 Constructing workflows..................... 17 3.1.4 Executing a workflow..................... 19 3.1.5 Remote execution over SSH.................. 20 3.2 Command line interface.......................... 21 3.2.1 Executing a workflow...................... 21 3.2.2 Executing a single component................. 24 3.2.3 Executing component test cases................ 25 3.2.4 Executing a workflow with the #! runner........... 26 3.2.5 Advanced command line usage and debugging........ 26 3.3 Apache Ant interface........................... 27 3.3.1 Executing a workflow...................... 27 3.4 Anduril graphical user interface.................... 29 3.5 Browsing the execution folder..................... 30 3.6 Isolated execution of a component instance in a workflow for debugging 32 3.7 Modes of execution........................... 33 3.7.1 Slurm.............................. 33 3.7.2 Prefix.............................