Changeset 373 for trunk/uk


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Timestamp:
Aug 8, 2007, 12:16:38 PM (16 years ago)
Author:
dominic
Message:
 
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1 edited

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

    r372 r373  
     1============================================================
     2General Information:
     3---------------------------
     4
     5This plugin imports raw data files and an experiment meta-data in the tab2mage specification into base. The tab2mage specification is provided by the microarray (link) informatics team at the EBI, Cambridge. The imported experiment can later be exported by the corresponding tab2mage export plugin. (link).
     6
     7The entry point for this plugin in base is the detail view page of an experiment. Hence, the user needs to create an experiment first and execute the plugin from this page by clicking on the import tab. The displayed wizards asked for the zip file containing the meta- data i.e. tab2mage file and the raw data files. Furthermore, the user’s  email server name could be specified to received notices of success or failure of the uploading or can be omitted to receive no message. 
     8
     9Installation
     10---------------
     11  - Place Tab2MageImporter.jar into the $BASE2_HOME/www/plugins/ directory on your BASE2 server.
     12  - 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 
     14  1. In the BASE web client, go to Administrate -> Plugins -> Definitions.
     15  2. Click New.
     16  3. In the dialog that opens,
     17    for class enter " uk.ac.ebi.nugo.plugins.Tab2MageImporter".
     18     for path enter the path to the plugin jar file, i.e. <BASE_HOME>/www/plugins/ Tab2MageImporter.jar
     19  4. Click Save.
     20  5. Click New again
     21  6. In the dialog that opens,
     22    for class enter " uk.ac.ebi.nugo.plugins.AnnotationTypeCvImporter".
     23    for path enter the path to the plugin jar file, i.e. <BASE_HOME>/www/plugins/ Tab2MageImporter.jar
     24  7. Click Save.
     25  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.
     26  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
     27 
     28  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
     30 
     31  General Installation instruction is available at:         http://base.thep.lu.se/chrome/site/doc/html/admindoc/plugin_installation/plugins.installation.html#plugins.installation
     32   
     33===========================================================
     34 Use
     35--------
     36 Note:
     37   --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.
     38 
     39  1. Platform supported  are: Affymetrix, Agilent, Genepix etc.
     40  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.
     41  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.
     42  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
     43  test first. 
     44  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.
     45  6. Open the detail view of the newly created experiment and click on the import tab.
     46  7. In the dialog that opens, leave the settings for Plugin and File format on auto-detect and click Next.
     47  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.
     48  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.
     49  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.
     50
     51  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.
     52
     53 ===========================================================
    154Dependencies:
    255--------------------
    3 -- Base 2.2.1 and above
    4 --AnnotationTypeCvImporter Plugin – For loading annotation types. The annotations are can annotate raw bio assays by default.
    5 --Reporter Importer - for loading reporter corresponding to the raw data file
    6 --Reporter map importer – for adding features to array design
    7 --Raw Data Importer Plugin – loads raw data. This must have a configuration that could import the raw data files.  Required for multi-channel experiments.
    8 -- mail.jar and activation. jar for messaging (included) - you could place these jar files in your tomcat class path (web-inf/lib)
     56  --Base 2.2.1 and above
     57  --AnnotationTypeCvImporter Plugin – For loading annotation types. The annotations are can annotate raw bio assays by      default.
     58  --Reporter Importer - for loading reporter corresponding to the raw data file
     59  --Reporter map importer – for adding features to array design
     60  --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.
     61  -- 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).
    962
    10 Please ensure that you have used all the plugins above appropriately before running Tab2Mage importer. Further documentation on
    11 AnnotationTypeCvImporter and AffyArrayDesignImproter plugin is available  on Base2plugin website and for others, please read base2 documentation.
     63  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.
    1264
    1365optional
    1466-------
    15 -- AffyArrayDesignImproter Plugin – for batch uploading affymetrix array designs.  Usefull to upload all array dsign in one go.
     67  -- AffyArrayDesignImproter Plugin – for batch uploading affymetrix array designs.  Useful to upload all array design in one go.
    1668
     69================================================================
     70AnnotationTypes and Cv Importer
     71----------------------------------------------
     72  --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.
     73  --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
     75===============================================================
    1776Email alert:
    1877---------------
    … …  
    2079
    2180Windows users:
    22 --------
    23 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).
    24 If this happens, you can simply ask your administrator to allow your machine to connect to the email server using port 20.
     81---------------------
     82  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).
     83  If this happens, you can simply ask your administrator to allow your machine to connect to the email server using port 20.
    2584
    26 The email alert should work on a linux / unix and may be mac machines.
    27 
    28 AnnotationTypes and Cv Importer
    29 ----------------------------------------------
    30 --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.
    31 --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.
    32 
     85  The email alert should work on a linux / unix and may be mac machines.
     86===============================================================
    3387What is not supported
    3488----------------------------------
    35 Pooled experiments are not suppported in this release. It would be supported in future releases.
     89Pooled experiments are not supported in this release. It would be supported in future releases.
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