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frankligy / SNAF

Splicing Neo Antigen Finder (SNAF) is an easy-to-use Python package to identify splicing-derived tumor neoantigens from RNA sequencing data, it further leverages both deep learning and hierarchical Bayesian models to prioritize certain candidates for experimental validation
MIT License
44 stars 8 forks source link

singularity running AltAnalyze bug #13

Closed frankligy closed 10 months ago

frankligy commented 2 years ago

When testing using the current singularity command, I found that it is less intuitive for first time users, specifically,

  1. you can not just specify bam folder, you need to specify as /usr/src/app/run/bam
  2. the AltAnalyze.sh file needs to be modified, should be cd /usr/src/app/run, as there is another root level /run folder
  3. maybe thinking about getting rid of --sandbox option, it is not for production usage