Migrate scripts for uploading data to new repository

[donkirkby]

Issue #5 is going to require changes to the upload scripts, so I'm going to move them into this repository. My plan is to put upload_QC_data_for_pending_miseq_runs.pl into the root directory, and put the rest of the scripts in a modules folder. They should all accept a settings object from Settings.pm that the QC report scripts use.

• Copy files from old repo to working folder, but don't commit.
• Review files, looking for sensitive data or workstation-specific paths. Move them to the settings file.
• Commit a broken version with minimal changes, just with sensitive things removed.
• Restructure scripts to be modules and accept the settings object.
• Test with some local data files uploading to test database, then commit.
• Replace die error handling to create an error file, clear the run, and move to the next run (issue Just fail single run when SQL fails #16).

[cbrumme]

upload_QC_data_for_pending_miseq_runs.pl doesn't seem to have run for the latest MiSeq run (141001_M01841_0078_000000000-AB843)

There's no qc_uploaded or qc_error file in that folder.

[donkirkby]

I had left an old copy of the crontab commands lying around, and Conan used that when he changed the schedule recently. I have deleted that copy, and set the commands back to the commands listed in the contributing instructions.
The data should be uploaded at noon today, and the report rerun at 1pm.

[cbrumme]

Still hasn't run as of noon on 9-Oct-2014

[donkirkby]

I made a mistake in the configuration. It's fixed and should run tomorrow at noon and 1pm.