Comments (3)
This is probably due to a typo we used to have in FRASER that was fixed a couple of weeks ago (padjBetaBinomial was changed to padjBetaBinomial). Can you please reinstall FRASER and update DROP? Then rerun the aberrantSplicing module.
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Isn't FRASER installed together with DROP? Do they need to be installed separately?
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Currently it's only checked if it's installed and if not it's installed but we do not check the correct version right now. So to have the latest version you would need to reinstall it.
@vyepez88 or @mumichae we should have a version number check in the init script. Problem here is that we have to make it correct depending on the bioc branch used eg for 1.0.2 for bioc3.10 and 1.1.3 for devel.
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Related Issues (20)
- Running pipeline offline in trusted research environemnt HOT 1
- lymphoblastoid cell lines datasets of gene counts
- Error running aberrantSplicing HOT 2
- Error in AberrantSplicing_pipeline_FRASER_04_fit_hyperparameters_FraseR_R HOT 3
- Error in MAE QC create matrix dna rna cor HOT 3
- CalledProcessError in installRPackages.R HOT 5
- Default running folder is out of space HOT 2
- Chunk options `#+echo` not correctly parsed HOT 1
- Incompatible with `Snakemake>=8` HOT 2
- Writing `rds` files as log can crash Snakemake execution HOT 1
- Error in h(simpleError(msg, call)) HOT 8
- requirementsR.txt referencing HEAD leads to irreproducibility / pipeline breaking HOT 3
- Problem running DROP HOT 2
- Annotation file asks for columns that shouldn't be needed HOT 2
- Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R HOT 10
- Pipeline fails with no significant results (AberrantSplicing_pipeline_FRASER_08_extract_results_FraseR_R) HOT 1
- Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R HOT 2
- Pipeline FAILS when specifying subsets of genes to test HOT 1
- useNames = NA is defunct HOT 4
- conda setup using yaml doesn't work HOT 1
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