Changeset 393
- Timestamp:
- Aug 14, 2007, 4:59:28 PM (16 years ago)
- File:
-
- 1 edited
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trunk/uk/ac/ebi/Tab2MageImporter/README.txt (modified) (6 diffs)
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trunk/uk/ac/ebi/Tab2MageImporter/README.txt
r392 r393 11 11 12 12 - Place Tab2MageImporter.jar into the $BASE2_HOME/www/plugins/ directory on your BASE2 server. 13 - Install as new plugins uk.ac.ebi.nugo.plugins.Tab2MageImporter and uk.ac.ebi.nugo.plugins.AnnotationTypeCvImporter which are 13 - Install as new plugins uk.ac.ebi.nugo.plugins.Tab2MageImporter and uk.ac.ebi.nugo.plugins.AnnotationTypeCvImporter which are both contained in $BASE_HOME/www/plugins/Tab2MageImporter.jar. 14 14 15 15 1. In the BASE web client, go to Administrate -> Plugins -> Definitions. … … 24 24 for path enter the path to the plugin jar file, i.e. <BASE_HOME>/www/plugins/ Tab2MageImporter.jar 25 25 7. Click Save. 26 The new plugins appears under the name "Tab2Mage Importer" and "AnnotationType and Cv Importer" respectively in the plugins list 27 8. Proceed to configure the "AnnotationType and Cv Importer" plugin. An example import file is provided here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/AnnotationTypeCvImporter/sampleimportfile.txt26 The new plugins appears under the name "Tab2Mage Importer" and "AnnotationType and Cv Importer" respectively in the plugins list and are now ready for use. 27 8. Proceed to configure the "AnnotationType and Cv Importer" plugin. An example import file is provided here: http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/AnnotationTypeCvImporter/sampleimportfile.txt 28 28 29 For other users to use the plugin as detailed in the next section, please share them to the appropriate users by manually setting the 29 For other users to use the plugin as detailed in the next section, please share them to the appropriate users by manually setting the permissions on the item. 30 30 31 31 32 General Installation instruction is available at: 32 General Installation instruction is available at: http://base.thep.lu.se/chrome/site/doc/html/admindoc/plugin_installation/plugins.installation.html#plugins.installation 33 33 34 34 =========================================================== … … 38 38 -- It is advisable not to execute the plugin as root but as a user with a specified quota. The quota must be enough to store files and create base items. 39 39 -- re- running the import plugin without having deleted the previously created directory from the zip file will make the Importer fail. 40 41 40 42 41 1. Platform supported are: Affymetrix, Agilent, Genepix etc. 43 2. Create all the array design used in the experiment as the BASE administrator. Array Design must then be shared to everyone or a suitable group that all the target users belong. 44 3. Create tab2mage spreadsheet and zip it together with the raw data files that make up the experiment. Note: no cdf file. Upload this file to your account on BASE (go to View -> Files -> Upload File). Image files may be supplied by the user and contained in the zip file. 45 Note: To avoid the laborious process of checking and formatting your tab2mage spreadsheet. Please use the example files: tab2mage- agilent, tab2mage- genepix and tab2mage- affymetrix, provided with the distribution as the spreadsheet template. For instance, the protocol section of your spreadsheet must have the protocol type specified.If not the plugin will fail. 46 4. To make sure you have all the required reporters and import configurations in place, import a single data file from the batch as a 47 test first. 48 5. If the previous step was successful, create a new experiment and specify the raw data type ( remember only affymetrix, genepix and agilent platfroms are supported) . Ensure that the experiment is of the same data type as the data in the files you want to import. Click the import tab from the plugin menu, select Tab2Mage Importer and click Next. 42 2. Create all the array design used in the experiment as the BASE administrator. Array Design must then be shared to everyone or a suitable group that all the target users belong. 43 3. Create tab2mage spreadsheet and zip it together with the raw data files that make up the experiment. Note: no cdf file. Upload this file to your account on BASE (go to View -> Files -> Upload File). Image files may be supplied by the user and contained in the zip file. 44 Note: To avoid the laborious process of checking and formatting your tab2mage spreadsheet. Please use the example files: tab2mage- agilent, tab2mage- genepix and tab2mage- affymetrix, provided with the distribution as the spreadsheet template. For instance, the protocol section of your spreadsheet must have the protocol type specified.If not the plugin will fail. 45 4. To make sure you have all the required reporters and import configurations in place, import a single data file from the batch as a test first. 46 5. If the previous step was successful, create a new experiment and specify the raw data type ( remember only affymetrix, genepix and agilent platfroms are supported) . Ensure that the experiment is of the same data type as the data in the files you want to import. Click the import tab from the plugin menu, select Tab2Mage Importer and click Next. 49 47 6. Open the detail view of the newly created experiment and click on the import tab. 50 48 7. In the dialog that opens, leave the settings for Plugin and File format on auto-detect and click Next. 51 8 On the next screen, Select the batch file that contains the raw data files, the Tab2Mage text file and the image file if 52 9. On the next screen, the ZipFile and Experiment parameters should already be configured now (as indicated by the black cross against them). Enter the name of your Tab2Mage file as a value for the "Tab2Mage FileName with Extension" parameter. Specifyyour email server if you want to receive notification on the success or failure of your experiment loading and click Next.53 10. On the next screen click Finish and wait for the job to complete. You will be shown the progress of the Tab2mage import in the 49 8 On the next screen, Select the batch file that contains the raw data files, the Tab2Mage text file and the image file if supplied and click Next. 50 9. On the next screen, the ZipFile and Experiment parameters should already be configured now (as indicated by the black cross against them). Enter the name of your Tab2Mage file as a value for the "Tab2Mage FileName with Extension" parameter. Specify your email server if you want to receive notification on the success or failure of your experiment loading and click Next. 51 10. On the next screen click Finish and wait for the job to complete. You will be shown the progress of the Tab2mage import in the dialog, with the page refreshing itself regularly. 54 52 55 When the import has finished, you can check and review the uploaded experiment by navigating thorughbase2 web client, using the 53 When the import has finished, you can check and review the uploaded experiment by navigating thorughbase2 web client, using the menu. If you have provided your email server name. You would receive an email on status of the import. 56 54 57 55 =========================================================== … … 59 57 -------------------- 60 58 --Base 2.2.1 and above 61 --AnnotationTypeCvImporter Plugin For loading annotation types. The annotations are can annotate raw bio assays by 59 --AnnotationTypeCvImporter Plugin For loading annotation types. The annotations are can annotate raw bio assays by default. 62 60 --Reporter Importer - for loading reporter corresponding to the raw data file 63 61 --Reporter map importer for adding features to array design 64 --Raw Data Importer Plugin loads raw data. This must have a configuration that could import the raw data files. Required for multi-channel experiments. The definition for the plug-in is available by default. The configuration should be done by administrator andshared to everyone or a suitable group that all the target users belong.65 -- if you want to use messaging, mail.jar and activation. jar for messaging is required- these jar files should be downloaded and 62 --Raw Data Importer Plugin loads raw data. This must have a configuration that could import the raw data files. Required for multi-channel experiments. The definition for the plug-in is available by default. The configuration should be done by administrator and shared to everyone or a suitable group that all the target users belong. 63 -- if you want to use messaging, mail.jar and activation. jar for messaging is required- these jar files should be downloaded and copied to your tomcat class path ( /webapps/(base)/web-inf/lib). 66 64 67 Please ensure that you have used all the plugins above appropriately before running Tab2Mage importer. Further information on 65 Please ensure that you have used all the plugins above appropriately before running Tab2Mage importer. Further information on AnnotationTypeCvImporter is available on Base2plugin website and for others, please read base2 documentation. 68 66 69 67 optional … … 74 72 AnnotationTypes and Cv Importer 75 73 ---------------------------------------------- 76 --the annotation type and cv loader plugin; uk.ac.ebi. nugo.plugins.CvAnnotationTypeImporter must be defined and configured. Both the plugin and its configured object must be shared to the user running the Tab2MageImporter. Defining and configuring the plugin should be done preferably by the administrator. The administrator should share the configuration to the users as well. Otherwisesuitable plugin configurations cannot be found and the import would fail.77 --A naming comparism of the annotation type in the flat file to the annotation type in base2 is actualized. Only non-existing annotation 74 --the annotation type and cv loader plugin; uk.ac.ebi. nugo.plugins.CvAnnotationTypeImporter must be defined and configured. Both the plugin and it's configured object must be shared to the user running the Tab2MageImporter. Defining and configuring the plugin should be done preferably by the administrator. The administrator should share the configuration to the users as well. Otherwise suitable plugin configurations cannot be found and the import would fail. 75 --A naming comparism of the annotation type in the flat file to the annotation type in base2 is actualized. Only non-existing annotation types are created. 78 76 79 77 =============================================================== … … 84 82 Windows users: 85 83 --------------------- 86 Your antivirus server and anti spam software may prevent you from sending email messages. This is because they must have been 84 Your antivirus server and anti spam software may prevent you from sending email messages. This is because they must have been configured to block all application requiring connection to your email sever on port 25 (smtp). 87 85 If this happens, you can simply ask your administrator to allow your machine to connect to the email server using port 20. 88 86
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