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jodyphelan/bootstrap-pathogen-genomics-tb

Last active May 2, 2023 20:02
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bootstrap-pathogen-genomics-tb
# mamba create -n tb-profiler python bwa "samtools>=1.12" "bcftools>=1.12" requests snpEff samclip trimmomatic parallel "delly>=0.8.7" "freebayes>=1.3.5" tqdm bedtools jinja2 filelock docxtpl
wget -O pathogen-genomics-tb-profiler-spec.txt https://gist.githubusercontent.com/jodyphelan/d220fb5ce97133ad5e5ae813edb7663d/raw/62bfeb6c0a6982bbb138d576e0d57bcac7605afe/pathogen-genomics-tb-profiler-spec
conda create --file pathogen-genomics-tb-profiler-spec.txt --name tb-profiler
source activate tb-profiler
pip install git+https://github.com/jodyphelan/TBProfiler/@dev
pip install git+https://github.com/jodyphelan/pathogen-profiler/@dev
cd ~/data/
mkdir tb
cd tb
wget -O tb_genomics_teaching.tgz --no-check-certificate https://tbdr.lshtm.ac.uk/static/tb_genomics_teaching.tgz
tar -xvf tb_genomics_teaching.tgz
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