Methylation beta-analysis wizard

[Nicklas Nordborg]

Implement a wizard that calculate beta-values for methylation bioassays.

See ticket #1418 for information about importing information about the methylation processing and items. Since it is likely that we may do more of this type of analysis in the future it was decided that the actual analysis that create beta-values should be implemented as a wizard. The wizard should assume that DNA aliquots, BeadChip? information and Methylation items have been imported as outlined in #1418.

The wizard will then start jobs on the new (container-based) cluster for running the Minfi pipeline that create beta-values, some PDF plots and other statistics for each sample.

[Nicklas Nordborg]

In 6867:

References #1419: Methylation beta-analysis wizard

Added a new section on the index page for "Other analysis" with a single subsection "Methylation".

[Nicklas Nordborg]

In 6868:

References #1419: Methylation beta-analysis wizard

Added an item list "Methylation beta-analysis" for Methylation derived bioassays that should be analyzed with the beta pipeline.

[Nicklas Nordborg]

In 6869:

References #1419: Methylation beta-analysis wizard

Added a wizard for selecting Methylation items for beta-analysis. The analysis is not yet implemented.

[Nicklas Nordborg]

In 6870:

References #1419: Methylation beta-analysis wizard

Added a job creator implementation. It should be able to register and submit jobs to the cluster, but there is no script yet so the jobs will always fail.

[Nicklas Nordborg]

In 6871:

References #1419: Methylation beta-analysis wizard

Added a simple script that so far only copy the IDAT files to the correct location in the project-archive directory.

[Nicklas Nordborg]

In 6872:

References #1419: Methylation beta-analysis wizard

Added a conteiner definition for the Minfo R package that should be used for the beta value calculations.

[Nicklas Nordborg]

In 6874:

References #1419: Methylation beta-analysis wizard

The R script now report progress to Reggie.

[Nicklas Nordborg]

In 6875:

References #1419: Methylation beta-analysis wizard

Updated the R script to output a file with QC values and other measurements.

[Nicklas Nordborg]

In 6876:

References #1419: Methylation beta-analysis wizard

Added a lot of annotations for storing the qc values.

[Nicklas Nordborg]

In 6877:

References #1419: Methylation beta-analysis wizard

Added thumbnails of the beta adjustment plot to the derived bioassay list and view page for Methylation items.

[Nicklas Nordborg]

In 6878:

References #1419: Methylation beta-analysis wizard

Added a flag annotation for recording some rare qc problems.

[Nicklas Nordborg]

In 6879:

References #1419: Methylation beta-analysis wizard

Started with the confirmation wizard. It displays some information from the analysis and options for re-analyze failed jobs or confirm. Registration of the results is not yet implemented.

[Nicklas Nordborg]

In 6880:

References #1419: Methylation beta-analysis wizard

Implemented confirmation and re-scheduling of finished beta-analysis jobs.

[Nicklas Nordborg]

In 6881:

References #1419: Methylation beta-analysis wizard

Implemented auto-confirmation.

[Nicklas Nordborg]

In 6882:

References #1419: Methylation beta-analysis wizard

Added methylation information to the case summary.

[Nicklas Nordborg]

In 6883:

References #1419: Methylation beta-analysis wizard

Fixed documentation of container definition file.

[Nicklas Nordborg]

In 6884:

References #1419: Methylation beta-analysis wizard

Since the run time for a job is ~1-2 minutes, we can decrease the interval between starting jobs from 30 to 5 seconds.

[Nicklas Nordborg]

In 6885:

References #1419: Methylation beta-analysis wizard

Modified help text for auto-confirm.

[Nicklas Nordborg]

In 6886:

References #1419: Methylation beta-analysis wizard

Adding a reference to the original script and authors.