Merge pull request #25 from mariogiov/devel

Various small updates
Merge pull request #26 from mariogiov/devel

Mostly addition of tests
Merge pull request #28 from mariogiov/devel

Change environmental variable PIPER_GLOB_CONF to PIPER_GLOB_CONF_XML; ad...
Merge pull request #29 from mariogiov/devel

Bugfix piper_qscripts_dir
Merge pull request #31 from mariogiov/devel

Eliminate symlinking rigamarole
Merge pull request #32 from mariogiov/devel

Bugfix / update requirements.txt
Merge pull request #36 from mariogiov/devel

Charon database and process tracking jazz
Merge pull request #39 from mariogiov/devel

Four-tiered directory structure; local process tracking; synchronization with Charon
Merge pull request #40 from mariogiov/devel

Bugfixes, track processes, sync with Charon
bug in order checking: first check if a project is in the restricted and then check if the project is on charon
added project name to error message
solved problem in conductor: not dealing properly with re-runs
commented part that was parsing all flowcell dir structure: saving more than 5 minutes per flowcellgit add ngi_pipeline/utils/parsers.pygit add ngi_pipeline/utils/parsers.py
added process single flowcell function to be sure to process a single flowcell per time
Conductor starts jobs on a flowcell per time and stores IDs into a local DB. On completion status is updated on Charon (still to be tested)
solved problem in Charon comunication in process_traking, wrong list of parameter and wrong return code
modify way in which db is returned in order to allow deletion of existing entries
started to work on updaiting charon at seq run level: only testing connection and getting run id.... I am going nuts here
script to clean charon at seq run level
pipeline now updates seq run once the alignment is done