gxa/ArrayExpressHTS — pull request #3 by andrewtikhonov (2012-02-29 11:12:46+00:00)
Title: Updates, enhancements and fixes

#3186, #3354:
- reorganised pipeline options, made them visible to users in the command syntax.
- reorganised R Cloud parameters into a single set of visible/usable options

#3187, #3347:
- added stop.on.warnings that allows detection of possible failures
earlier. However if used it would narrow the amount of experiments
that can be successfully processed.
- improved error handling within the ArrayExpressHTS
- added log.error instead of log.info where necessary

#3196:
- cleaned the package of some analysis code as well as some outdated code

#3408:
- reimplemented problematic searching and downloading of .seq.sdrf.txt files

#3409:
- fixed problematic handling of "NA" or "missing" nominal length values from ENA

#3410:
- made the pipeline automatically detect "Organism" from SDRF and filter using
a selected value.

#3412:
- reworked reading from SDRF to cover most of the "flexible formatting" cases

#3413:
- improved creation of R Cloud computation cluster, widened usage of retries.

#3414:
- made a number of reference preparation tasks be able to run in parallel and
not affect each other.

#3415:
- added proper functions to work with environment variables

#3351:
- fixed the "count" method to properly read fields of bam files

#3416:
- fixed the annotation processing following Ensembl update.

#3417:
Update documentation, prepare for submission into Bioc
- updated package help pages
- updated descriptions and references
- updated package vignette documentation
- slightly reorganised the structure of the document
- rewritten some sections
- added a few new sections
- added examples where needed