Changeset 496


Ignore:
Timestamp:
Nov 28, 2007, 5:12:26 PM (16 years ago)
Author:
dominic
Message:

updated read me file

Location:
trunk/uk/ac/ebi/Tab2MageImporter
Files:
1 deleted
1 edited

Legend:

Unmodified
Added
Removed

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

    r472 r496  
    33---------------
    44
    5   - Place Tab2MageImporter.jar into the $BASE2_HOME/www/plugins/ directory on your BASE2 server.
    6   - 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.
     5  - Place Tab2MageImporter.jar, activation.jar, ebi-plugins-utils.jar, mail.jar, bloader.jar and AnnotationTypeCvImporter.jar into the $BASE2_HOME/www/plugins/ directory on your BASE2 server.
     6 
     7  - Install as new plugins uk.ac.ebi.nugo.plugins.Tab2MageImporter
     8  Note: If you get a class Loader error while installing the importer, you have two options:
     9 
     10  i) Upgrade to BASE 2.4.6  or
     11  ii) Place all the jar files above in your base installation classpath - i.e. : $BASE2_HOME/web-inf/lib, restart the tomcat server and proceed to install the plugin. In step (3) below, do not specify the plugin's path. Note that BASE do not recommend this approach but it's just a work around for a bug in base versions earlier than 2.4.6.
     12 
     13  - If you have not already defined  and configured a working AnnotationTypeCvImporter.jar, then install as new plugin    uk.ac.ebi.nugo.plugins.AnnotationTypeCvImporter.
    714 
    815  1. In the BASE web client, go to Administrate -> Plugins -> Definitions.
    … …  
    1724  7. In the dialog that opens,
    1825    for class enter " uk.ac.ebi.nugo.plugins.AnnotationTypeCvImporter".
    19     for path enter the path to the plugin jar file, i.e. <BASE_HOME>/www/plugins/ Tab2MageImporter.jar
     26    for path enter the path to the plugin jar file, i.e. <BASE_HOME>/www/plugins/ AnnotationTypeCvImporter.jar
    2027    if you have chosen another location for the jar, you should adapt to that.
    2128  8. Click Save.
    … …  
    2734  11. 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. (sharing it to group 'Everyone' should be sufficient in most cases).
    2835
    29   12. PERMISSION for users and/or the tab2mage importer plugin is important to run an import successfully. Please check the WARNING in the 'USE' section below 
     36  12. PERMISSION for users and/or the tab2mage importer plugin is important to run an import successfully. Please check the WARNING in the 'USE' section below
    3037
    3138  General Installation instruction is available at: http://base.thep.lu.se/chrome/site/doc/html/admindoc/plugin_installation/plugins.installation.html#plugins.installation
    32   
     39 
    3340===========================================================
    3441 Use
    3542=======
    3643Warning:
    37 ----
     44-----------
    3845  --  User with a specified quota must have the required capacity to store files and create base items. Note that user can have unlimited quota.
    39   --  Re- running the import plugin without having deleted the previously created directory from the zip file will make the Importer fail. Please delete from the trash can too.
    40   --  Note that in its current implementation, only one RawDataImporter plugin configuration can be used during the import process. This means that raw data files must be      consistent throughout. (this might be an issue when using different scanner versions).
     46  --  Note that in its current implementation, only one RawDataImporter plugin configuration can be used during the import process. This means that raw data files must be consistent throughout. (this might be an issue when using different scanner versions).
    4147  --  The importer can be executed in a validation mode, to first validate the tab2mage spreadsheet before loading in to BASE. Please see the instructions on the GUI   when running the plugin for guidance.
    4248
    4349  Permission
    4450  ----------------
    45   --  Make sure that the user running Tab2Mage Importer plugin has enough permission to do so. With the default Roles settings in BASE, User and PowerUser roles have     not enough permission to run the plugin successfully. There are two options available:
    46   i.  Edit the priviledge of the power user or user role in base.
    47   ii. Assign permissions to the Tab2Mage Importer Plugin. The plugin does not use permission by default, but the administrator can set permission for the plugin. Please see :http://base.thep.lu.se/chrome/site/doc/html/admindoc/plugin_installation/plugins.permissions.html for setting plugin permissions.
     51  --  Make sure that the user running Tab2Mage Importer plugin has enough permission to do so. With the default Roles settings in BASE, User and PowerUser roles have not enough permission to run the plugin successfully. There are two options available:
     52  i.)  Edit the priviledge of the power user or user role in base.
     53  ii.) Assign permissions to the Tab2Mage Importer Plugin. The plugin does not use permission by default, but the administrator can set permission for the plugin. Please see :http://base.thep.lu.se/chrome/site/doc/html/admindoc/plugin_installation/plugins.permissions.html for setting plugin permissions.
    4854 
    4955  1. Platforms supported  are: Affymetrix, Agilent, Genepix
    50   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.
     56  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.
    5157  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.
    5258  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. Running the import in validation mode will help identify all potential problems.
    53   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. 
     59  - For more information see the spreadsheet rules available here: .http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/tab2mage-spreadsheet-rules.txt
     60  4. To ensure you have all the required reporters and import configurations in place, import a single data file from the batch as a test first. 
    5461  5. If the previous step was successful, create a new experiment  and specify the raw data type ( remember only affymetrix, genepix and agilent  platforms 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.
    5562  6. Open the detail view of the newly created experiment and click on the import tab.
    5663  7. In the dialog that opens,  leave the settings for Plugin and File format on auto-detect and click Next.
    5764  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.
    58   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.
    59   10. If you wish, you can change the default filename for the "Save Validation Report As" parameter. If the validation report already exists indicate whether it should overwritten with the "overwrite" parameter.
    60   11. To run the importer in validation mode only, set 'Run validation' parameter to true and click Next.
    61   12. 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.
     65  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.
     66  10. Specficy a name for the directory to store unzipped files. This directory cannot be re-used on re-running the importer.
     67  11. To run the importer in validation mode only, set 'Run validation' parameter to true 
     68  12.  If you wish, you can change the default filename for the "Save Validation Report As" parameter. If the validation report already exists indicate whether it should overwritten with the "overwrite" parameter.and click Next.
     69  13. 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.
    6270
    6371  When the import has finished, you can check and review the uploaded experiment by navigating through base2 web client, using the menu. If you have provided your email server name. You would receive an email message on the status of the import.
    6472
    65 =========================================================
    66 Pooling Implementation
    67 --------------------------------
    68 The tab2mage importer runs in a pooled or non- pooled state.
    69 A pooling protocol - Protocol[pool] must be specified for experiments that involve pooling, otherwise the importer would run in a non-pool state.
    70 
    71 One stage pooling - > biosource to sample, sample to extract or extract to labeled extract is fully supported
    72 
    73 Multiple stage pooling: biosource to sample and sample to extract supported.  Note that Multi stage pooling involving labeled extract is not supported.
    74 
    75 Please check pooling notes link on the download page for more information
    76 
    77 For usability and consistency on the biomaterial user interface, do run the same experiment twice. An imported experiment (with raw data and meta-data) that involves pooling may only be loaded once.
    78 
    79  ===========================================================
    80 AnnotationTypes and Cv Importer
    81 ----------------------------------------------
    82   --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.
    83   --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.
    84 
    85 ===============================================================
    86 Limitations and Known Issues
    87 ----------------------------------
    88 i. Only one raw data importer plugin configuration can be used at any one time during an experiment import.
    89 This means that all raw  data files in a tab2mage.zip archive should have the same data header. For Raw datafile from Genepix (or .gpr files) and Agilent, there is a certain level of polymorphism that may occur should scanner models used in a experiment run different versions of the software. Users will have to harmonize the files to one layout in order to upload the Experiment in BASE2 using the current plugin.
    90 
    91 ===============================================================
    92 Email alert:
    93 ---------------
    94 To receive an email alert on the success or failure of your experiment loading,
    95 
    96 Windows users:
    97 ---------------------
    98   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).
    99   If this happens, you can simply ask your administrator to allow your machine to connect to the email server using port 25.
    100 
    101   The email alert works on a linux / unix and may be mac machines.
    102 ==============================================================
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