Changeset 393


Ignore:
Timestamp:
Aug 14, 2007, 4:59:28 PM (14 years ago)
Author:
dominic
Message:

updated readme txt

File:
1 edited

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  • trunk/uk/ac/ebi/Tab2MageImporter/README.txt

    r392 r393  
    1111
    1212  - 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    both contained in $BASE_HOME/www/plugins/Tab2MageImporter.jar.
     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.
    1414 
    1515  1. In the BASE web client, go to Administrate -> Plugins -> Definitions.
     
    2424    for path enter the path to the plugin jar file, i.e. <BASE_HOME>/www/plugins/ Tab2MageImporter.jar
    2525  7. Click Save.
    26   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
     26  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
    2828 
    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.
     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.
    3030
    3131 
    32   General Installation instruction is available at:         http://base.thep.lu.se/chrome/site/doc/html/admindoc/plugin_installation/plugins.installation.html#plugins.installation
     32  General Installation instruction is available at: http://base.thep.lu.se/chrome/site/doc/html/admindoc/plugin_installation/plugins.installation.html#plugins.installation
    3333   
    3434===========================================================
     
    3838  -- 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.
    3939  --  re- running the import plugin without having deleted the previously created directory from the zip file will make the   Importer fail.
    40  
    41  
     40   
    4241  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.
    4947  6. Open the detail view of the newly created experiment and click on the import tab.
    5048  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      supplied  and  click Next.
    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.  Specify      your 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    dialog, with the page refreshing itself regularly.
     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.
    5452
    55   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.
     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.
    5654
    5755 ===========================================================
     
    5957--------------------
    6058  --Base 2.2.1 and above
    61   --AnnotationTypeCvImporter Plugin – For loading annotation types. The annotations are can annotate raw bio assays by      default.
     59  --AnnotationTypeCvImporter Plugin – For loading annotation types. The annotations are can annotate raw bio assays by default.
    6260  --Reporter Importer - for loading reporter corresponding to the raw data file
    6361  --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 and    shared 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    copied to your tomcat class path ( /webapps/(base)/web-inf/lib).
     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).
    6664
    67   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.
     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.
    6866
    6967optional
     
    7472AnnotationTypes and Cv Importer
    7573----------------------------------------------
    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. Otherwise    suitable 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    types are created.
     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.
    7876
    7977===============================================================
     
    8482Windows users:
    8583---------------------
    86   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).
     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).
    8785  If this happens, you can simply ask your administrator to allow your machine to connect to the email server using port 20.
    8886
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