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jodyphelan/Install latest tb-profiler.md

Last active December 2, 2021 15:27
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Install latest tb-profiler.md

Install latest tb-profiler

  1. Use the yml file to create the tb-profiler conda env
wget https://gist.githubusercontent.com/jodyphelan/92ec9b18f5b929bd1637d56568abbd0a/raw/ae52641f56cfa982c0a2febade10b2b7b882b6fa/tb-profiler-env.yaml
conda env create -f tb-profiler-env.yaml
  1. Activate env
 conda activate tb-profiler-dev
  1. Install tb-profiler
git clone  https://github.com/jodyphelan/TBProfiler.git
cd TBProfiler
python setup.py install
  1. Download database files
git clone https://github.com/jodyphelan/tbdb.git
cd tbdb
git checkout who_list
tb-profiler create_db --csv who.dr_mutations.csv --watchlist who.watchlist.csv --other_annotations who.other_mutations.csv  --prefix who
tb-profiler load_library who
  1. Profiler sample
tb-profiler profile -1 /path/to/reads_1.fq.gz -2 /path/to/reads_2.fq.gz --db who --prefix sample_name
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