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jodyphelan/tb-profiler-tests.sh

Last active November 18, 2024 15:36
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tb-profiler-tests.sh
test_env=testing
mamba create -y -n $test_env python bwa "samtools>=1.12" "bcftools>=1.12" requests snpEff jq samclip gatk4 trimmomatic parallel "delly>=1.1.7" "freebayes==1.3.6" tqdm minimap2 bedtools jinja2 samclip kmc pilon lofreq filelock mash docxtpl dsk pysam rich-argparse joblib iqtree pydantic tomli itol-config sourmash
conda activate $test_env
pip install rich_argparse
mamba install flask celery redis sqlalchemy psycopg2
pip install redis flask_sqlalchemy flask_login flask_session flask_wtf email_validator
pip install --force-reinstall git+https://github.com/jodyphelan/TBProfiler.git@dev
pip install --force-reinstall git+https://github.com/jodyphelan/pathogen-profiler.git@dev
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