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HenrikBengtsson / aroma.seq

🔬 R package: aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework
https://github.com/HenrikBengtsson/aroma.seq
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pileup2seqz() requires sequenza (<= 2.1.2) #48

Open HenrikBengtsson opened 4 years ago

HenrikBengtsson commented 4 years ago

Issue

The new sequenza 3.0.0 does no longer implement Sequenza using Python. If used here, we'll get errors such as:

Error in system.file("exec", "sequenza-utils.py", package = "sequenza",  : 
  no file found

Tasks

  1. [x] Add assertion that we've got sequenza (<= 2.1.2) installed.
stopifnot(packageVersion("sequenza") <= "2.1.2")
  1. [ ] Update aroma.seq to support sequenza (>= 3.0.0), which BTW, is a pain to install on our legacy TIPCC system, cf. https://github.com/HenrikBengtsson/Costello-PSCN-Seq/issues/24