Update .gitignore

Update .gitignore to ignore emacs cruft.
Merge pull request #376 from hammer/patch-1

Update .gitignore to ignore emacs cruft.
Rsync files from completed flowcells from sequencer dump to analysis machine.
Added Alla's affiliation.
Illumina sequencer support: start processing on remote bcbio analysis server. Updates to server to support additional configuration
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Add finished to timing information.
Revert "Add finished to timing information."

This reverts commit a98b71e9e7381542e42cadc22b2994b1efd32982.

Accidentally removed _setup_resources. Thanks to @hammer for
noticing.
Re-add timing finished message to RNA-seq pipeline.
Added note about .pydistutils.cfg causing installation problems.
Added RNA-seq slides from Feb. 2014 BIG meeting.
Update configuration.rst

The GATK Resource Bundle URL appears to have changed
Automated sample processing: ensure fastq inputs are sorted before merging for consistent pairs. Set default algorithm parameters using existing templates in sample YAML config
Merge pull request #379 from hammer/patch-2

Update configuration.rst with new GATK Resource Bundle URL
Swallow gzip error message when checking sizes for bwa processing since not indicative of an actual issue. Clean up ability to find fastq files in processing directories. Add support for dm3 genome.
Update ipython-cluster-helper to version 0.2.17.

This contains a fix for non-KB based LSF resource usage
configurations.
Provide checks for pre-aligned input BAM files: ensure sample names match and chromosomes match. #370 #378
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
Move data files used in exome analysis pipeline into bcbio S3 bucket
Automated processing using a tornado server: ensure we can handle local multicore parallelism by launching external subprocess instead of inside background thread.