jerowe

#Nginx

    #nginx.conf
    location /foo {
        proxy_set_header X-Real-IP $remote_addr;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header Host $http_host;
        proxy_set_header X-NginX-Proxy true;
 proxy_pass http://127.0.0.1:3000/foo;

jerowe

---
global:
    - indir: data/raw 
    - outdir: data/Analysis 
    - reference: /scratch/Reference_Genomes/Public/Vertebrate_other/Anolis_Carolinensis/AnoCar2.0/anoCar2.fa
    - bowtie_tmp_dir: "data/Analysis/{$sample}/Bowtie2/tmp"
    - file_rule: (Sample.*)$
    - by_sample_outdir: 1
    - find_by_dir: 1
rules:

jerowe

---
use:
    - Slurp
    - Data::Dumper
global:
    - indir: data/processed/rename
    - outdir: data/processed
    - PROCESSED: data/processed
    - ROOT: data/processed
    - file_rule: (Sample.*)$

jerowe

#!/bin/bash

DATE=`date +%Y-%m-%d--%H-%M-%S`

export RefGenDir="/scratch/Reference_Genomes/Public"
export SoftwareDir="/scratch/gencore/software/bin/build_indices"

read -r -d '' TEMPLATE <<EOF
#HPC queue=adserial
#HPC commands_per_node=12

jerowe

# loading raw data
gunzip lane1_NoIndex_L001_R1_001.fastq.gz
gunzip lane1_NoIndex_L001_R2_001.fastq.gz
gunzip lane1_NoIndex_L001_R3_001.fastq.gz

# fix barcode headers to match R1 headers
cat lane1_NoIndex_L001_R2_001.fastq | sed 's/2:N:[0-9]\+:/1:N:0:/g' > barcodes.fixed.fastq

# validate mapping file
validate_mapping_file.py -m CDC1_MAP.txt -o corrected_map

jerowe

#!/usr/bin/env python2

import argparse
import subprocess
import os

parser = argparse.ArgumentParser(description='Install things')
parser.add_argument('--instdir',  help='you must supply an installdir')
parser.add_argument('--requirements',  nargs='?', help='optionally supply a list of packages to install', required=False)
parser.add_argument('--channels',  nargs='+', help='optionally supply a list of channels to search', required=False)

jerowe

use strict;
use warnings;

use Module::Build 0.28;
use File::Find;

our @files = ();
find( \&wanted, ".");

sub wanted {

jerowe

var path = require('path');
var Promise = require('bluebird');
var fs = require('fs');

var app = require(path.resolve(__dirname, '../server/server'));

// Add your datasource here
var ds = app.datasources.chemgenDS;

//Write out your models here

jerowe

let mapleader="\\"
syntax on
filetype plugin indent on

call plug#begin('~/.vim/plugged')

Plug 'noahfrederick/vim-neovim-defaults'

Plug 'junegunn/vim-easy-align'
Plug 'SirVer/ultisnips' | Plug 'honza/vim-snippets'

jerowe

name: gencore_variant_detection_1.0
channels:
- bioconda
- r
- nyuad-cgsb
dependencies:
- perl-hpc-runner-slurm=2.58
- perl-biox-workflow=1.10
- perl-biox-workflow-plugin-fileexists=0.13
- perl-biox-workflow-plugin-filedetails=0.11