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sanger-pathogens / iva

de novo virus assembler of Illumina paired reads
http://sanger-pathogens.github.io/iva/
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Fix #93 by switching from smalt to bowtie2. #94

Closed donkirkby closed 4 years ago

donkirkby commented 4 years ago

I tried to change as little as possible beyond the switch from smalt to bowtie2, but I did need to make three sets of changes:

  1. Some of the test data files needed to change, because bowtie2 behaved slightly differently.
  2. The docker file couldn't find that old version of Java, it needed some more dev packages, and bowtie2 needed to have a default version of python available.
  3. I switched the docker file to COPY . iva/ instead of cloning from GitHub, because I can't test on your GitHub branch. You could switch that back if you want to.
donkirkby commented 4 years ago

I'm closing this for now, because bowtie2 mapping takes longer, and the -r option of smalt is a smaller change to solve the same problem.