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cgat-developers / cgat-flow

cgat-flow repository
MIT License
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updated mapping to make tophat run #48

Closed Acribbs closed 5 years ago

Acribbs commented 5 years ago

@sebastian-luna-valero this commit fixes a problem when running tophat or tophat2. The genome build does not work because the conda environment does not specify tophat2. In addition to this, samtools needs to be included as part of the tophat2 conda environment.

Acribbs commented 5 years ago

This makes changes to code that was added to PipelineMapping.py in this commit https://github.com/cgat-developers/cgat-flow/commit/909632a99c086aaa12d7e244f45e34c787b7830b#diff-ef4d6ca67395164fcee0a268e8bb6524

@sebastian-luna-valero it seem as though when you introduced this code to modify tophat conda env you removed the statement variable. I have fixed this but I have also realised that we dont test Tophat or Tophat2, im not sure if people are really using these anymore though (im analysing legacy data)

sebastian-luna-valero commented 5 years ago

Looks good to me, thanks!

Yes, we don't want to add tophat to the testing. Reminder in the link: https://twitter.com/lpachter/status/937055346987712512