Comments (3)
vyepez88
commented on July 18, 2024
1
Hi Joseph, indeed, we are aware of all those issues and are working on addressing them. We'll come back to you in the next few days.
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jaicher
commented on July 18, 2024
It looks like #537 will hopefully address the immediate issue I ran into with the updated version of FRASER.
I would still hope for some kind of predictable versioning of DROP's dependencies. If one were to publish an analysis using DROP, how should they report the version of OUTRIDER/FRASER/tMAE that they used? How could someone else wanting to reproduce their analysis set up a matching environment that didn't integrate changes made to these dependencies?
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vyepez88
commented on July 18, 2024
Hi Joseph. Thanks again for raising these concerns. With v 1.3.4 we have tried to be more robust to different versions of packages and dependencies. We now install only specific versions. We recommend you install 1.4.0, which further contains improvements to FRASER.
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Related Issues (20)
- 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
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- 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
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