Jody Phelan jodyphelan
jodyphelan
/ ebiDownload.pl
Created
June 17, 2019 12:05
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| #! /usr/bin/perl | |
| use warnings; | |
| use strict; | |
| if (scalar @ARGV !=1){print "\nebiDownload <acc_list>\n\n"; exit;} | |
| open F, $ARGV[0] or die; | |
| while(<F>){ | |
| chomp; |
jodyphelan
/ .bashrc
Created
June 17, 2019 11:02
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| # ~/.bashrc: executed by bash(1) for non-login shells. | |
| # see /usr/share/doc/bash/examples/startup-files (in the package bash-doc) | |
| # for examples | |
| # If not running interactively, don't do anything | |
| case $- in | |
| *i*) ;; | |
| *) return;; | |
| esac |
jodyphelan
/ tb_setup.sh
Last active
June 17, 2019 12:27
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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 ~/ |
jodyphelan
/ base
Created
June 17, 2019 10:43
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| name: base | |
| channels: | |
| - conda-forge | |
| - bioconda | |
| - defaults | |
| dependencies: | |
| - _r-mutex=1.0.0=anacondar_1 | |
| - asn1crypto=0.24.0=py37_0 | |
| - bcftools=1.9=ha228f0b_4 | |
| - binutils_impl_linux-64=2.31.1=h6176602_1 |
jodyphelan
/ rsync
Created
May 22, 2019 10:49
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| rsync -avz --exclude-from ~/exclude_list.txt jody 10.18.0.21:/opt/storage2/jody/laptop_snpapshots/ | |
| <head exlude_list.txt> | |
| /jody/Library | |
| /jody/Pictures | |
| /jody/Music | |
| /jody/VirtualBox VMs | |
| /jody/example_data | |
jodyphelan
/ gist:aaa778d1031ded4e8834409033badd86
Created
May 21, 2019 12:08
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| vi /etc/apache2/sites-available/000-default.conf | |
| sudo a2enmod proxy && sudo a2enmod proxy_http && sudo service apache2 restart |
jodyphelan
/ tb-profiler
Created
May 6, 2019 09:23
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| TBProfiler report | |
| ================= | |
| The following report has been generated by TBProfiler. | |
| Summary | |
| ------- | |
| ID: por7B | |
| Date: Mon May 6 09:31:27 2019 | |
| Strain: lineage4.3.4.1 |
jodyphelan
/ tb-profiler
Created
May 6, 2019 09:23
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| TBProfiler report | |
| ================= | |
| The following report has been generated by TBProfiler. | |
| Summary | |
| ------- | |
| ID: por7B | |
| Date: Mon May 6 09:31:27 2019 | |
| Strain: lineage4.3.4.1 |
jodyphelan
/ gist:614698a7e60fe4f5e52c3cc96e0d2012
Last active
March 27, 2019 14:31
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| #!/usr/bin/env sh | |
| export CPP_INCLUDE_PATH=${CONDA_PREFIX}/include | |
| export CXX_INCLUDE_PATH=${CONDA_PREFIX}/include | |
| export CPLUS_INCLUDE_PATH=${CONDA_PREFIX}/include | |
| export LIBRARY_PATH=${CONDA_PREFIX}/lib | |
| conda install -y htslib libboost wget samtools bcftools bwa minimap2 bowtie2 tqdm parallel trimmomatic | |
| cd /tmp/ | |
| wget https://github.com/dellytools/delly/archive/v0.8.1.tar.gz | |
| tar -xvf v0.8.1.tar.gz |
jodyphelan
/ samtools stats
Created
March 20, 2019 23:09
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| # Get data | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/009/SRR2099969/SRR2099969_1.fastq.gz | |
| wget ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR209/009/SRR2099969/SRR2099969_2.fastq.gz | |
| wget ftp://ftp.ensemblgenomes.org/pub/release-32/bacteria//fasta/bacteria_0_collection/mycobacterium_tuberculosis_h37rv/dna/Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz | |
| gunzip Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa.gz | |
| mv Mycobacterium_tuberculosis_h37rv.ASM19595v2.dna.toplevel.fa H37Rv.fa | |
| # Get software | |
| wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2 && tar -xvf samtools-1.9.tar.bz2 && cd samtools-1.9/ && make && cd .. | |
| wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.5/bowtie2-2.3.5-linux-x86_64.zip && unzip bowtie2-2.3.5-linux-x86_64.zip |