Jillian Rowe jerowe
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| --- | |
| global: | |
| - indir: data/processed | |
| - outdir: data/analysis | |
| - analysis_dir: data/analysis | |
| - root: data/analysis | |
| - samtools: "data/analysis/{$sample}/samtools" | |
| - samtools_dir: "data/analysis/{$sample}/samtools" | |
| - picard: "data/analysis/{$sample}/picard" | |
| - picard_dir: "data/analysis/{$sample}/picard" |
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| let mapleader="\\" | |
| syntax on | |
| filetype plugin indent on | |
| call plug#begin('~/.vim/plugged') | |
| Plug 'noahfrederick/vim-neovim-defaults' | |
| Plug 'junegunn/vim-easy-align' | |
| Plug 'kassio/neoterm' |
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| #!/usr/bin/env bash | |
| #SBATCH -p serial | |
| #SBATCH --job-name=metagenomics | |
| #SBATCH --time=00:10:00 | |
| # Output and error files | |
| #SBATCH -o job.%J.out | |
| #SBATCH -e job.%J.err | |
| #SBATCH --nodes=1 | |
| #SBATCH --ntasks=1 | |
| #SBATCH --cpus-per-task=6 |
jerowe
/ metagenomics-pipeline.sh
Last active
January 12, 2017 05:01
— forked from twaddlac/metagenomics-pipeline.sh
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| #!/usr/bin/env bash | |
| #SBATCH -p serial | |
| #SBATCH --job-name=metagenomics | |
| #SBATCH --time=00:10:00 | |
| # Output and error files | |
| #SBATCH -o job.%J.out | |
| #SBATCH -e job.%J.err | |
| #SBATCH --nodes=1 | |
| #SBATCH --ntasks=1 | |
| #SBATCH --cpus-per-task=6 |
jerowe
/ IGV-2.3.91.eb
Last active
September 11, 2017 09:23
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| easyblock = 'Conda' | |
| name = 'IGV' | |
| version = '2.3.91' | |
| homepage = 'http://www.broadinstitute.org/software/igv/' | |
| description = """ The Integrative Genomics Viewer (IGV) is a high-performance visualization | |
| tool for interactive exploration of large, integrated genomic datasets. It supports a wide | |
| variety of data types, including array-based and next-generation sequence data, and genomic annotations. """ |
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| { | |
| "hits" : { | |
| "hits" : [ | |
| { | |
| "_score" : 1, | |
| "_type" : "submission", | |
| "_source" : { | |
| "project" : "MY_AWESOME_PROJECT", | |
| "hpc_meta" : { | |
| "jobs" : [ |
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| { | |
| "timed_out" : false, | |
| "took" : 2, | |
| "hits" : { | |
| "hits" : [ | |
| { | |
| "_id" : "AVxxv6EvgklmRgejGgFv", | |
| "_score" : 1, | |
| "_index" : "hpcrunner", | |
| "_source" : { |
jerowe
/ easybuild_bootstrap_install.sh
Last active
August 27, 2017 08:15
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| #!/bin/bash | |
| # Define help function | |
| function help(){ | |
| echo "EasyBuild Bootstrap - Bootstrap method of installing easybuild"; | |
| echo "Usage example:"; | |
| echo "easybuild-bootstrap (-e|--easybuild_install_base) char [(-h|--help) boolean] [(-E|--environment_modules)] [(-L|--lmod)] [(-b|--eb_version) char] [(-l|--lmod_version) char] [(-m|--em_version) char]"; | |
| echo "Options:"; | |
| echo "-h or --help boolean: Displays this information."; | |
| echo "-E or --environment_modules: Include Environment Modules."; |
jerowe
/ vinu_r_conda_env.yml
Last active
June 20, 2017 07:58
conda env create -p /scratch/vinu/software/bioconductor_minfi/ -f vinu_r_conda_env.yml
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| name: bioconductor_minfi | |
| channels: | |
| - bioconda | |
| - r | |
| - defaults | |
| - conda-forge | |
| - nyuad-cgsb | |
| dependencies: | |
| - bioconductor-biobase=2.34.0 | |
| - bioconductor-minfi=1.20.0 |
jerowe
/ easybuild_config_environment_modules.cfg
Created
August 27, 2017 07:38
Minimal configuration for use of easybuild with environment modules
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| [MAIN] | |
| # Enable debug log mode (def False) | |
| #debug= | |
| # Enable info log mode (def False) | |
| #info= | |
| # Enable quiet/warning log mode (def False) | |
| #quiet= | |
| [basic] | |
| # Print build overview incl. dependencies (full paths) (def False) |