| | 1 | = Updating to Reggie 4.12 = |
| | 2 | |
| | 3 | === New Hisat pipeline for secondary analysis === |
| | 4 | |
| | 5 | '''Do not update to Reggie 4.12 if there are items waiting in the ''Start Tophat and Cufflinks'' wizard!! ''' |
| | 6 | |
| | 7 | Due to changes in the flow control those items will disappear from the list. |
| | 8 | |
| | 9 | === New annotation on alignment software and protocols === |
| | 10 | |
| | 11 | A new annotation type, `AlignmentType` has been added. Find existing software and protocols with `Type=Alignment` and set the `AlignmentType` annotation to `Tophat`. |
| | 12 | |
| | 13 | Create a new software and protocol item for the Hisat pipeline. They should have `Type=Alignment` and `AlignmentType=Hisat`. Keep the `Add as project default` checkbox checked and the `Replace existing default` unchecked. |
| | 14 | |
| | 15 | === Update the pipeline scripts === |
| | 16 | |
| | 17 | Install the latest pipeline scripts. The `alignment_statistics.sh` script has been updated with support for Hisat output files. Download the script from http://baseplugins.thep.lu.se/browser/other/pipeline/trunk and save it on the computation cluster in the location specified by the `<pipeline-scripts><path>` setting in `reggie-config.xml`. |
