Changes between Initial Version and Version 1 of net.sf.basedb.reggie/notes426


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Timestamp:
Apr 14, 2020, 9:30:22 AM (2 years ago)
Author:
Nicklas Nordborg
Comment:

Started to write update instructions for Reggie 4.26

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  • net.sf.basedb.reggie/notes426

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     1= Updating to Reggie 4.26 =
     2
     3== A. Before updating Reggie ==
     4
     5=== 1. Install a new Picard version on the prime cluster ===
     6
     7We need Picard version 2.22.3 or higher since it fixes a problem with !NovaSeq data files and the !CheckIlluminaDirectory
     8function. Verify that the `<picard><path>` setting `reggie-config.xml` is poiting to the correct installation directory
     9and modify if needed. Picard can be downloaded from https://github.com/broadinstitute/picard/releases.
     10
     11== B. Update Reggie ==
     12
     13Update Reggie to version 4.26 as usual. Do not forget to run the Installation wizard.
     14
     15== C. After updating Reggie ==
     16
     17=== 1. Upload CTG sample sheet template ===
     18
     19Upload the `CTG_SampleSheet.xlsx` file to the `/home/SCANB/Templates` directory in BASE.
     20
     21=== 2. Import variant annotations ===
     22
     23In the **RNA library preparation and analysis**/**Variant calling pipeline** section,
     24run the **Import variants for existing variant call raw bioassays** wizard. This wizard
     25will import variants that are found in some interesting genes as annotations to existing
     26raw bioassay items and will take several minutes to run. The same functionality is
     27included in the regular variant calling script so the wizard is not needed in the future.
     28See #1229 for more information.
     29
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