gxa/ArrayExpressHTS — pull request #1 by andrewtikhonov (2011-10-27 10:47:58+00:00)
Title: A number of fixed and enhancements combined into a single commit

- Ticket #3178: added proper warning logs, aded warnings in the package as necessary
- Ticket #3171: updated the package to work with the updated ENA interface
- Ticket #3171: added handling of "not defined" values in FASTQ fields in ENA XML
- Ticket #3171: added handling of "scientific sample name" in ENA XML
- added a routine to obtain all HTS accessions from AE
- Ticket #3137: added support for predefined ArrayExpressHTS.xxx options
- Ticket #3137: reworked the discovery of tools to use ArrayExpressHTS.xxx options and
also to perform discovery in the predefined locations.
- Ticket #2828: added support for new versions of tools, made necessary changes in the
package to support new tools output & format as necessary, added a "stable"
toolset & workflow and an "experimental" toolset & workflow activatable via
an option
- Ticket #3172: updated the final ExpressionSet R object to include the version of the
reference that was used to produce he object.
- Ticket #3138: added and automatic fix for the double "Y" region, which needs to be
removed be fore the reference is indexed.
- Ticket #3137: updated some of the initDefaultEnvironment.Rd documentation
- Ticket #3173: updated the gtf2txt tool to handle new format of reference
- Ticket #3180: added cleaning of cluster nodes prior to loading of the pipeline
- Ticket #3179: added propagation of global and package options to cluster nodes