Update main.py

By default on Mac OS X the maximum number of files a process can open is 10,240. Unless the number 50,000 was chosen for a good reason, I suggest we change `target_procs` to `10240` to ensure a better out-of-the-box experience for Mac users.

The alternative would be to add a check for OS X before lowering `target_procs`.
Merge pull request #372 from hammer/patch-1

Mac OS X: use a lower value of target_procs
Ensure process setting handled correctly when maximum limits are infinite
Only pass on and perform ploidy evaluation during haploid conversion if output has a genotype call. Fixes #370
Prepare combined fastq files from a flowcell, merging samples on multiple lanes and outputs split by bcl2fastq. Create final configuration file describing samples for processing. Update galaxy upload to handle inputs provided through YAML configuration instead of directly via nglims calls.
Merge branch 'master' of github.com:chapmanb/bcbio-nextgen
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