Changes between Version 75 and Version 76 of uk.ac.ebi.Tab2MageImporter


Ignore:
Timestamp:
Apr 14, 2008, 5:11:22 PM (14 years ago)
Author:
Jari Häkkinen
Comment:

Updated links.

Legend:

Unmodified
Added
Removed
Modified
  • uk.ac.ebi.Tab2MageImporter

    v75 v76  
    1515== Prerequisites ==
    1616
    17 Base 2.2 and above. For the latest release [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/ChangeLog.txt Change Log], you would need BASE 2.4.6. See the documentation section for more details. [[BR]]
     17Base 2.2 and above. For the latest release [source:plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/ChangeLog.txt Change Log], you would need BASE 2.4.6. See the documentation section for more details. [[BR]]
    1818
    1919Reporter Importer Plugin - Required for loading Reporters [[BR]]
     
    2525''The definition for the above plug-ins is available by default in Base 2. The plugins should be configured by a Base 2 administrator and shared to everyone or a suitable group of target users. [[BR]]''
    2626
    27 [http://lev.thep.lu.se/trac/baseplugins/wiki/uk.ac.ebi.AnnotationTypeCvImporter AnnotationTypeCvImporter Plugin] – Required for loading annotation types.  The plugin must have a proper configuration defined to import an annotation type file created by the Tab2MageImporter plugin when parsing the tab2mage file.[[BR]]
     27[wiki:uk.ac.ebi.AnnotationTypeCvImporter AnnotationTypeCvImporter Plugin] – Required for loading annotation types.  The plugin must have a proper configuration defined to import an annotation type file created by the Tab2MageImporter plugin when parsing the tab2mage file.[[BR]]
    2828
    2929'''Please''' ''ensure that you have used all the plugins above appropriately, before running Tab2Mage importer. Read the README file in the documentation section for further details.''
    3030
    31 Click [http://lev.thep.lu.se/trac/baseplugins/wiki/uk.ac.ebi.AnnotationTypeCvImporter AnnotationTypeCvImporter] for further information on Annotation Type and Cv Importer plugin and for other plugins, please read base2 documentation.
     31Click [wiki:uk.ac.ebi.AnnotationTypeCvImporter AnnotationTypeCvImporter] for further information on Annotation Type and Cv Importer plugin and for other plugins, please read base2 documentation.
    3232
    3333Also, do make sure that Array Design(s) corresponding to the one(s) referenced in the Array[accession] field of the tab2mage file have been properly created in BASE2. If not, the plugin will fail. For all non-Affymetrix Array Designs,this means that Reporters have been loaded and Feature to Reporter Map have been attached to Array Designs. Those tasks can be only be achieved if the above plugins have been properly set up and configured.
     
    3535=== Optional ===
    3636
    37 [http://baseplugins.thep.lu.se/wiki/uk.ac.ebi.AffyArrayDesignBatchImporter AffyArrayDesignBatchImporter Plugin ].
     37[wiki:uk.ac.ebi.AffyArrayDesignBatchImporter AffyArrayDesignBatchImporter Plugin ].
    3838– for batch uploading affymetrix array designs.  Useful to upload all array designs used in an experiment in one go before running the Tab2Mage Importer.[[BR]]
    3939
     
    4242
    4343||'''Installation and Use'''|| '''Known Issues/Features''' ||'''Sample Tab2Mage Import Work Flow'''||'''Pooling Note'''||
    44 ||[http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README.txt README.txt]||[http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/README-KnownIssuesandFeatures.txt README.txt]||[http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/simplied%20process.txt Affymetrix]||[http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/pooling.txt README.txt] ||
     44|| [source:plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/README.txt README.txt] || [source:plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/README-KnownIssuesandFeatures.txt README.txt] || [source:plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/simplied%20process.txt Affymetrix] || [source:plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/pooling.txt README.txt] ||
    4545
    4646==== FAQs ====
    4747
    48 [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/Importer%20FAQ.txt Tab2Mage Import FAQ].
     48[source:plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/Importer%20FAQ.txt Tab2Mage Import FAQ].
    4949
    5050==== Tab2Mage Spreadsheets ====
    5151
    5252||'''Rules for Creating Spreadsheet'''|| '''Sample Spreadsheets''' ||
    53 ||[http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/tab2mage-spreadsheet-rules.txt Rules]||[http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/tab2mage-%20affymetrix.txt?format=raw  Affymetrix]|[http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/ta2mage-%20agilent.txt?format=raw Agilent]|[http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/tab2mage-%20genepix.txt?format=raw Genepix]||
     53|| [source:plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/tab2mage-spreadsheet-rules.txt Rules] || [http://baseplugins.thep.lu.se/browser/plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/tab2mage-%20affymetrix.txt?format=raw  Affymetrix] | [http://baseplugins.thep.lu.se/browser/plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/ta2mage-%20agilent.txt?format=raw Agilent] | [http://baseplugins.thep.lu.se/browser/plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/tab2mage-%20genepix.txt?format=raw Genepix] ||
     54
    5455
    5556== Maintenance plan ==
     
    8283
    8384||'''Version''' ||'''Plugin jar file'''||'''Dependent jars'''||'''Change Log'''||
    84 ||2||[http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/Tab2MageImporter.jar?format=raw Tab2MageImporter.jar]||[http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/lib/bloader.jar?format=raw bloader.jar] | [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageExporter/ebi-plugins-utils.jar?format=raw ebi-plugins-utils.jar] | [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/lib/AnnotationTypeCvImporter.jar?format=raw AnnotationTypeCvImporter.jar] [[BR]] [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/lib/mail.jar?format=raw mail.jar] | [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/lib/activation.jar?format=raw activation.jar]||[http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/ChangeLog.txt Change Log]||
    85 ||1||[http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter/Tab2MageImporter-1.0.jar?format=raw Tab2MageImporter-1.0.jar]|| || ||
     85|| 2 || [http://baseplugins.thep.lu.se/browser/plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/Tab2MageImporter.jar?format=raw Tab2MageImporter.jar] || [http://baseplugins.thep.lu.se/browser/plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/lib/bloader.jar?format=raw bloader.jar] | [http://baseplugins.thep.lu.se/browser/plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageExporter/ebi-plugins-utils.jar?format=raw ebi-plugins-utils.jar] | [http://baseplugins.thep.lu.se/browser/plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/lib/AnnotationTypeCvImporter.jar?format=raw AnnotationTypeCvImporter.jar] [[BR]] [http://baseplugins.thep.lu.se/browser/plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/lib/mail.jar?format=raw mail.jar] | [http://baseplugins.thep.lu.se/browser/plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/lib/activation.jar?format=raw activation.jar] || [http://baseplugins.thep.lu.se/browser/plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/ChangeLog.txt Change Log] ||
     86|| 1 || [http://baseplugins.thep.lu.se/browser/plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter/Tab2MageImporter-1.0.jar?format=raw Tab2MageImporter-1.0.jar] || || ||
    8687'''Sample archives''': [http://www.ebi.ac.uk/~oyeniran/pages/download.html#archives Genepix, Agilent, Affymetrix and GenePix with Pooling]
    8788
    8889==== Source code ====
    89 [http://lev.thep.lu.se/trac/baseplugins/browser/trunk/uk/ac/ebi/Tab2MageImporter SVN][[BR]]
     90[source:plugins/base2/uk.ac.ebi.tab2mage/trunk/Tab2MageImporter SVN][[BR]]
    9091
    9192== License ==