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| wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh | |
| bash Miniconda3-latest-Linux-x86_64.sh -b | |
| curl https://gist.githubusercontent.com/jodyphelan/d54eb38b211a0a49d898e7f54e3fa613/raw/a97a3720a62dee4b54b1bd79d3f6e2ab201ea0f3/.bashrc > .bashrc | |
| ~/miniconda3/bin/conda config --add channels defaults | |
| ~/miniconda3/bin/conda config --add channels bioconda | |
| ~/miniconda3/bin/conda config --add channels conda-forge | |
| ~/miniconda3/bin/conda install -y trimmomatic bwa samtools bcftools gatk4 delly parallel tqdm | |
| git clone https://github.com/jodyphelan/TBProfiler.git | |
| cd TBProfiler && python setup.py install | |
| cd ~/ | |
| git clone https://github.com/jodyphelan/pathogen-profiler.git | |
| cd pathogen-profiler && python setup.py install | |
| cd ~/ | |
| tb-profiler update_tbdb | |
| wget https://gist.githubusercontent.com/jodyphelan/761a9158469585dd509134ec1755c752/raw/93f21ed56416b2ffd4604ef87ace45cd8101c5e3/ebiDownload.pl | |
| mv ebiDownload.pl ~/miniconda3/bin | |
| chmod 755 ~/miniconda3/bin/ebiDownload.pl | |
| mkdir vcf results bam | |
| wget https://gist.githubusercontent.com/jodyphelan/92bb087a95af1064981b8629afdb6514/raw/815ec4c50edcaa7a83a4a5ff89b5b46492367d6f/run_sample.sh |
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