Jody Phelan jodyphelan
jodyphelan
/ collate-script.py
Created
March 20, 2025 15:38
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| from collections import defaultdict | |
| import os | |
| from pathogenprofiler import filecheck | |
| import csv | |
| import pathogenprofiler as pp | |
| from tqdm import tqdm | |
| import json | |
| import ntm_profiler as ntmp | |
| from ntm_profiler.models import ProfileResult, SpeciesResult |
jodyphelan
/ ntm-profiler-dev
Last active
March 13, 2024 11:12
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| wget https://raw.githubusercontent.com/jodyphelan/TBProfiler/dev/conda/linux-latest.txt | |
| conda create --name ntm-profiler-dev --file linux-latest.txt | |
| conda activate ntm-profiler-dev | |
| pip install --force-reinstall git+https://github.com/jodyphelan/pathogen-profiler.git@dev | |
| pip install --force-reinstall git+https://github.com/jodyphelan/ntm-profiler.git@dev | |
| ntm-profiler update_db |
jodyphelan
/ parse mutations
Created
February 7, 2024 13:11
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| conda activate tb-profiler-dev | |
| pip install --force-reinstall git+https://github.com/jodyphelan/pathogen-profiler.git@dev | |
| pip install --force-reinstall git+https://github.com/jodyphelan/TBProfiler.git@dev | |
| git clone https://github.com/jodyphelan/tbdb.git | |
| cd tbdb | |
| # move the parsed_who_mutations.csv and genes.csv to the current directory | |
| # cp ~/temp/parsed_who_mutations.csv . | |
| # cp ~/temp/genes.csv . |
jodyphelan
/ TB-Profiler-Dev
Last active
March 7, 2024 15:14
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| wget https://raw.githubusercontent.com/jodyphelan/TBProfiler/dev/conda/linux-latest.txt | |
| conda create --name tb-profiler-dev --file linux-latest.txt | |
| conda activate tb-profiler-dev | |
| pip install --force-reinstall git+https://github.com/jodyphelan/pathogen-profiler.git@dev | |
| pip install --force-reinstall git+https://github.com/jodyphelan/TBProfiler.git@dev | |
| # If you want to use a custom refrence | |
| tb-profiler update_tbdb --match_ref ~/refgenome/NC000962.3.fa --branch test | |
| # If you want to install ntm-profiler |
jodyphelan
/ nanopore
Created
July 19, 2023 15:37
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| # This file may be used to create an environment using: | |
| # $ conda create --name <env> --file <this file> | |
| # platform: linux-64 | |
| @EXPLICIT | |
| https://conda.anaconda.org/biocore/linux-64/mafft-7.245-0.tar.bz2 | |
| https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 | |
| https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2 | |
| https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2022.10.11-h06a4308_0.conda | |
| https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 | |
| https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2 |
jodyphelan
/ portugal-microbiome-setup.sh
Last active
July 4, 2023 20:11
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| # 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-microbiome-profiler-spec.txt https://gist.githubusercontent.com/jodyphelan/92d8a63f498434f1c30bd48fcff8f8bb/raw/79d24bc7dcc72589145fbb5079ad108fe7fd51f7/microbiome-spec.txt | |
| conda create --file pathogen-genomics-microbiome-profiler-spec.txt --name microbiome | |
| conda activate microbiome | |
| pip install multiqc | |
| mv Module6 Module6_old | |
| mkdir Module6 | |
| cd Module6 | |
| wget -O microbiome_data.tgz --no-check-certificate https://tbdr.lshtm.ac.uk/static/microbiome_data.tgz | |
| tar -xvf microbiome_data.tgz |
jodyphelan
/ bootstrap-pathogen-genomics-microbiome
Last active
May 14, 2023 18:13
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| # 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-microbiome-profiler-spec.txt https://gist.githubusercontent.com/jodyphelan/92d8a63f498434f1c30bd48fcff8f8bb/raw/79d24bc7dcc72589145fbb5079ad108fe7fd51f7/microbiome-spec.txt | |
| conda create --file pathogen-genomics-microbiome-profiler-spec.txt --name microbiome | |
| source activate microbiome | |
| cd ~/data/ | |
| mkdir microbiome | |
| cd microbiome | |
| wget -O microbiome_data.tgz --no-check-certificate https://tbdr.lshtm.ac.uk/static/microbiome_data.tgz | |
| tar -xvf microbiome_data.tgz |
jodyphelan
/ microbiome-spec.txt
Created
May 14, 2023 17:17
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| # This file may be used to create an environment using: | |
| # $ conda create --name <env> --file <this file> | |
| # platform: linux-64 | |
| @EXPLICIT | |
| https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 | |
| https://conda.anaconda.org/conda-forge/noarch/_r-mutex-1.0.1-anacondar_1.tar.bz2 | |
| https://repo.anaconda.com/pkgs/main/linux-64/ca-certificates-2021.7.5-h06a4308_1.tar.bz2 | |
| https://conda.anaconda.org/bioconda/linux-64/entrez-direct-15.6-he881be0_1.tar.bz2 | |
| https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 | |
| https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2 |
jodyphelan
/ bootstrap-pathogen-genomics-tb
Last active
May 2, 2023 20:02
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| # 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 |
jodyphelan
/ pathogen-genomics-tb-profiler-spec
Last active
May 2, 2023 15:57
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| # This file may be used to create an environment using: | |
| # $ conda create --name <env> --file <this file> | |
| # platform: linux-64 | |
| @EXPLICIT | |
| https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 | |
| https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.24-ha878542_0.tar.bz2 | |
| https://conda.anaconda.org/conda-forge/noarch/font-ttf-dejavu-sans-mono-2.37-hab24e00_0.tar.bz2 | |
| https://conda.anaconda.org/conda-forge/noarch/font-ttf-inconsolata-3.000-h77eed37_0.tar.bz2 | |
| https://conda.anaconda.org/conda-forge/noarch/font-ttf-source-code-pro-2.038-h77eed37_0.tar.bz2 | |
| https://conda.anaconda.org/conda-forge/noarch/font-ttf-ubuntu-0.83-hab24e00_0.tar.bz2 |
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