NationalGenomicsInfrastructure/ngi_pipeline — pull request #131 by guillermo-carrasco (2014-11-27 17:16:03+00:00)
Title: Run tracker - First working prototype

Tested in `preproc1.scilifelab.se`, with runs directory `/srv/illumina/HiSeq_X_data/test_run_tracker`

In there you can find this test:

```
/srv/illumina/HiSeq_X_data/test_run_tracker/
└── 141127_SOMETHING_001_AH0000CCXX
├── Data
├── Reports
│ └── Report.htm
├── test.fastq.gz
└── ThisFile.xml
```

If you want me to showcase all possible scenarios (i.e a run in progress, a run finished with demultiplexing in progress, etc), I think it is better is you come to my desk and I can show you.

The general case for a finished looks like this:
```
(master)hiseq.bioinfo@preproc1:~/opt/ngi_pipeline/scripts (run_tracker)$ python run_tracker.py
2014-11-27 18:13:25,083 - Run tracker - INFO - Checking run 141127_SOMETHING_001_AH0000CCXX
2014-11-27 18:13:25,083 - Run tracker - INFO - Starting BCL to FASTQ conversion and demultiplexing for run 141127_SOMETHING_001_AH0000CCXX
2014-11-27 18:13:25,083 - Run tracker - INFO - Building bcl2fastq command
2014-11-27 18:13:25,098 - Run tracker - INFO - BCL to FASTQ conversion and demultiplexing started for run 141127_SOMETHING_001_AH0000CCXX on 2014-11-27 18:13:25.098389
2014-11-27 18:13:25,114 - Run tracker - INFO - Started transfer of run 141127_SOMETHING_001_AH0000CCXX on 2014-11-27 18:13:25.114087
2014-11-27 18:13:25,736 - Run tracker - INFO - Adding run 141127_SOMETHING_001_AH0000CCXX to /home/hiseq.bioinfo/log/transfer.tsv
```