| | 1 | = Updating to Reggie 4.40 = |
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| | 4 | === 1. New array design === |
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| | 6 | Create a new array design, `hg38gencode41filtered` for representing the new GTF that should be used by !StringTie/2023. |
| | 7 | * Make sure that the `Set as project default` checkbox is set. |
| | 8 | * The `Pipeline` annotation of the new array design should be set to `RNAseq/StringTie/2023`. The annotation type must be enabled for the ARRAYDESIGN item type first (this is done by the Reggie installation wizard but it is better to prepare this before installing the new version). |
| | 9 | * Upload the `gencode.v41.primary_assembly.annotation.ucsc.filtered.gtf` and link it to the new array design. Place the GTF in the `/home/SCANB/GTF` directory. BASE should report that the file contains 88838 features. |
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| | 11 | === 2. Create new software items for Hisat/2023 and !StringTie/2023 === |
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| | 13 | New software items are needed for `Masking`, `Alignment` and `Feature extraction` subtypes. The new items should describe the new 2023 pipeline. Make sure that the `Add as project default` checkbox is selected and that the `Replace existing default` is not. Annotate the new items with the correct `Pipeline` annotation (eg. `RNAseq/Hisat/2023` or `RNAseq/Hisat/StringTie`). Also set the `AlignmentType` and `ExpressionType` values. |
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| | 15 | Also set the the `Pipeline` annotation for existing software items, or they will not be found the the wizards. |
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| | 18 | === 3. New configuration for Reggie and the Job scheduler extension === |
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| | 20 | The Job scheduler extesion version 1.7 need to be installed. Create a new entry in the `opengrid-config.xml` for accessing the Slurm-based cluster. The `slurm-accounting-disabled` flag should be set unless accounting has been enabled before this update. |
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| | 22 | Create a new `<host>` entry in `reggie-config.xml` that is linked to the new cluster definition. Fill the `<host>` entry with configuration settings that are needed for running the Hisat/2023 and !StringTie/2023 analysis steps. The configuration file that ships with Reggie should have an example that is is more or less complete already. |
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| | 24 | === 4. Update Reggie to 4.40 === |
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| | 27 | === 5. Disable auto-processing for the Hisat/2023 pipeline === |
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| | 29 | Until we know how stable the new pipeline is it better to manually start. To disable auto-processing set `AutoProcessing=Disable` for the item list named `Hisat/2023 Pipeline`. The `StringTie/2023 Pipeline` doens't have to be disabled. |
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| | 31 | === 6. Test the new pipeline === |
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| | 33 | Fix problems if there are any. |
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