Removed alignment dependancy on fastqc from workflow

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12016 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
working on hl7 parser

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12018 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
First version of the editable matrix for AnimalDB, in the 'data viewer' screen.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12019 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
compilation fix for xQTL

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12020 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Removed the additional exceptions from matrixviewer handlerequest again, and adjusted previous fix accordingly. Changed the handlerequestdelegationexception to only have a constructor for any exception.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12021 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Added 	public boolean email(.. String fileAttachment, ByteArrayOutputStream outputStream,..) Sending email with xls attachment. 


git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12025 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Added wormqtl experiment information in an html table

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12026 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Added new text for the wormqtl about page

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12027 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Changes for MVID db: Added dynamic content, sorted by publication year, used 'onset' as phenotype, ...

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12028 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Reworking wormqtl gui:
- Renamed and moved screens
- Started adding dataset id's to experiment overview (todo: finish and linkout)
- Removed many toplinks (todo: need Help page with links to tutorials, API, docs, etc)
- Moved references and sponsors from Home to About
- Added Contact page template (todo: add content)
- Introduced copy action in build script to keep 'about' and 'contact' HTML files out of Webcontent root

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12029 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Date format fix for remove animal plugin

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12030 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Added dataset ids plus linkouts to experiment overview in wormqtl

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12031 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Moved generic importer to modules/import/plugins and renamed to biobank importer.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12032 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
removed generic importer.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12033 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Added another column in the option of the mapping so that we can import in multiple tables on column of the excel .

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12034 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Added a new row in the mapping table which indicated the type of the Entity for BBMIR. E.g. the type of measurement could be ontology terms.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12035 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
adding new function for automatically generating R-scripts based on the mapping that was done in the previous step. There are several new files that are introduced including a FreemMrker generator and a template that holds the generated R-scripts.  R-scripts can be run in R-console using R-api.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12036 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Bugfix: Fixed array out of bound error if location was specified in add animal plugin

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12037 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Moved generic importer back to apps/catalogue/ because it depends on various datamodel components such as auth, compute, pheno and organization which not every application uses.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12038 42de9c89-b41c-0410-9fa9-f33e7b6bda7a
Saving multiple values option in mappings files.

git-svn-id: http://www.molgenis.org/svn/molgenis_apps/trunk@12039 42de9c89-b41c-0410-9fa9-f33e7b6bda7a