=================================================== MeLuDi extension package README =================================================== == Requirements == 1. BASE 3.4 or later. == Introduction == This package is an extension package to BASE that can be used to simplify biosource and sample registration. * The homepage for this extension: http://baseplugins.thep.lu.se/wiki/net.sf.basedb.meludi == Installation and updating == 1. Download the meludi-*.tar.gz file. 2. Unpack the downloaded file to a directory of your choice. 3. Copy the 'meludi.jar' file to your BASE plug-ins directory. Eg. the directory specified by the 'plugins.dir' setting in 'base.config'. 4. Edit and copy configuration files to their correct location. See config/readme.txt for more information. If this is a first-time installation shut down BASE and run 'updatedb.sh' script so that additional reporter annotations and raw data columns are created. 5. Log in to BASE as a user with Administrator privileges. 6. Go to 'Administrate->Plug-ins & Extensions->Overview' page. Run the installation wizard and select to install/update 'meludi.jar'. 7. Create a project and set it as the active project. This step is optional but is recommended. Running MeLuDi without an active project will generate warning messages later on. MeLuDi 1.2 uses a counter service to display numbers of different item selections on the main page, and will only work in a project named "MeLuDi". 8. Go to the Extensions->MeLuDi menu. Select the 'Installation wizard' If the 'MeLuDi' menu is not visible try BASE->Reload permissions menu. 9. It should display a list with several error message about missing items. Click on the "Create missing items" button to create them. If no project was created in step 6, all annotation types will be shared with the 'PatientCurator' group, otherwise only some will be shared to the group and some will be shared to the active project. 10. Manual fixes. Check the release information if any manual changes are needed to items that already exists in BASE. 11. Done. == Using == MeLuDi appears as a menu entry in the Extensions menu. All operations are available on that page. * Installation wizard: This entry is available if the logged in user is an 'Administrator' and will perform some basic checks that items that are needed by MeLuDi exists and have been properly configured. Items that doesn't exist can be created automatically. * Personal information registration wizard: This entry is available for 'Administrators' and members of the 'PatientCurator' group. It is used to register new patients and cases. It can also be used to update an existing case with patient info. * Specimen tube registration wizard: This entry is available for those with permission to create samples. It is used to register new specimen tubes for cases that are not yet in BASE. * DNA/RNA extraction wizards: These entries are available for those with permission to create samples. They are used to register new extracts from specimens, and update quantity values for input RNA/DNA. == Compiling == To compile this package you also need: 1. Ant 1.9 2. Java 1.7 Follow these instructions: 1. Download the source code from the subversion repository. See http://baseplugins.thep.lu.se/wiki/net.sf.basedb.meludi for instructions. 2. Type `ant download-lib` to automatically download the BASE core JAR files that are needed for compilation. You can also do this manually by copying the base-*.jar files from the BASE installation directory (/www/WEB-INF/lib/) to the ./lib/compile directory. 3. Type 'ant' to compile the code and generate the 'meludi.jar' file in the project directory. 4. Use 'ant package' to create a downloadable tar.gz package. Tip: If you need different values for any of the properties defined in the 'build.xml' file, create a file named 'build.properties' and set the values there.