Changeset 407 for trunk/uk/ac/ebi/Tab2MageImporter/README.txt
- Timestamp:
- Aug 23, 2007, 2:56:34 PM (16 years ago)
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- 1 edited
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trunk/uk/ac/ebi/Tab2MageImporter/README.txt (modified) (5 diffs)
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trunk/uk/ac/ebi/Tab2MageImporter/README.txt
r402 r407 33 33 34 34 =========================================================== 35 35 36 Use 36 37 -------- … … 38 39 -- 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 40 -- re- running the import plugin without having deleted the previously created directory from the zip file will make the Importer fail. 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).41 41 -- 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). 42 -- - Make sure that the user running Tab2Mage Importer plugin has enough permissions to do so. With the default Roles settings in BASE, User and PowerUser have not enough permissions to run the plugin successfully. 42 43 43 1. Platform supported are: Affymetrix, Agilent, Genepix etc.44 1. Platform supported are: Affymetrix, Agilent, Genepix 44 45 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. 45 46 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. … … 56 57 57 58 =========================================================== 59 58 60 Dependencies: 59 61 -------------------- 60 --Base 2.2.1 and above 61 --AnnotationTypeCvImporter Plugin For loading annotation types. This must have a configuration that could import an annotation types (.txt) file. 62 --Reporter Importer - for loading reporter corresponding to the raw data file 63 --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 base iinstallatiion claass path /web-inf/lib folder. 62 63 - Base 2.2 and above 66 64 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 -Reporter Importer Plugin - Required for loading Reporters 66 67 Reporter Map Importer Plugin Required for mapping features to Reporters when defining an Array Design 68 69 Raw Data Importer Plugin Required for loading raw data and import values associated to BASE rawBioassays. This is a critical requirement, for multi-channel experiments, before running the Tab2MageImporter. Users must ensure that raw data import plugin has been properly configured and is able to import a raw datafile of the type of the submission. 70 71 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. 72 73 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. 74 75 Please ensure that you have used all the plugins above appropriately, before running Tab2Mage importer. Click AnnotationTypeCvImporter for further information on Annotation Type and Cv Importer plugin and for other plugins, please read base2 documentation. 76 77 Also, 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. 68 78 69 79 optional 70 80 ------- 71 -- AffyArrayDesignImproter Plugin for batch uploading affymetrix array designs. Useful to upload all array design in one go. 81 - AffyArrayDesignBatchImporter Plugin . for batch uploading affymetrix array designs. Useful to upload all array designs used in an experiment in one go before running the Tab2Mage Importer. 82 83 If you want to use messaging, mail.jar and activation. jar is required- these jar files should be downloaded and copied to your base installation class path /web-inf/lib folder. 72 84 73 85 ================================================================ 86 74 87 AnnotationTypes and Cv Importer 75 88 ---------------------------------------------- … … 78 91 79 92 =============================================================== 93 94 Limitations and Known Issues 95 ---------------------------------- 96 i. Currently, Pooling event represented in tab2mage format are not supported. It would be supported from next plugin release . 97 98 ii. Only one raw data importer plugin configuration can be used at any one time during an experiment import. 99 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. 100 101 iii. Agilent support: 102 103 Some Agilent Feature Extraction raw data files can be loaded but not all. BASE2.4.0 plugin API differs from BASE2.3.0 plugin API and even if users can successfully import Agilent Raw data files in BASE2.4, the tab2mage import plugin has yet to be updated to reflect the changes in the BASE plugin API. All the infrastructure is being modified to take advantage of the API modification and Agilent support will be available shortly. We will post an updated version of the plugin when ready and make an announcement through the base mailing lists 104 105 =============================================================== 106 80 107 Email alert: 81 108 --------------- … … 85 112 --------------------- 86 113 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 If this happens, you can simply ask your administrator to allow your machine to connect to the email server using port 2 0.114 If this happens, you can simply ask your administrator to allow your machine to connect to the email server using port 25. 88 115 89 116 The email alert should work on a linux / unix and may be mac machines. 90 ===============================================================91 What is not supported92 ----------------------------------93 Pooled experiments are not supported in this release. It would be supported in future releases.
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