| /* | |
| This file includes default values for Teton. | |
| */ | |
| process { | |
| executor = 'slurm' | |
| queue = 'teton,moran' | |
| scratch = params.slurm_use_scratch | |
| time = 60.m | |
| clusterOptions = '--account healthdatasci' |
| #!/usr/bin/env bash | |
| # ~/.bashrc: executed by bash(1) for non-login shells. | |
| # If not running interactively, don't do anything | |
| [ -z "$PS1" ] && return | |
| # don't put duplicate lines in the history. See bash(1) for more options | |
| # ... or force ignoredups and ignorespace | |
| HISTCONTROL=ignoredups:ignorespace |
| #! /usr/bin/env python3 | |
| if __name__ == '__main__': | |
| import os | |
| import sys | |
| import time | |
| import argparse as ap | |
| import sevenbridges as sbg | |
| from sevenbridges.errors import SbgError |
| #! /bin/bash | |
| GS_PATH=$1 | |
| # Copy Local | |
| gsutil -q cp ${GS_PATH} ./ | |
| LOCAL_FILE=$(basename ${GS_PATH}) | |
| OUTDIR="./" | |
| if echo "${LOCAL_FILE}" | grep ".rg.sorted.bam"; then | |
| OUTDIR="./nanopore" | |
| else |
| #! /bin/bash | |
| SCRUBBER_DB=${SCRUBBER_SHARE}/data/human_filter.db | |
| # Current scrubber | |
| echo "Run test on current Scrubber" | |
| which scrub.sh | |
| scrub.sh test | |
| echo "Run test on PR Scrubber" |
| #! /usr/bin/env bash | |
| # https://www.ncbi.nlm.nih.gov/nuccore/1798174254 | |
| WUHAN=29903 | |
| while IFS=$'\t' read -r POSITION SAMPLE_ID ANALYSIS SEQUENCING_COVERAGE ASSEMBLY_COVERAGE; do | |
| if [ "${POSITION}" == "POSITION" ]; then | |
| printf "%s\t%s\t%s\t%s\t%s\n" "sample_id" "clearlabs_cov" "observed_cov" "mapped_coverage" "unmapped_coverage" | |
| else | |
| FASTQ=$(ls fastq/ | grep ${SAMPLE_ID}) | |
| if [ -f "fastq/${FASTQ}" ]; then |
| from urllib2 import Request, urlopen, URLError | |
| import json | |
| import math | |
| import sys | |
| import os | |
| import socket | |
| import optparse | |
| | |
| def arg_parser(): | |
| cwd_dir = os.getcwd() |
| >X17403.1:c80631-76903 Human cytomegalovirus strain AD169 complete genome | |
| ATGTTTTTCAACCCGTATCTGAGCGGCGGCGTGACCGGCGGTGCGGTCGCGGGTGGCCGGCGTCAGCGTT | |
| CGCAGCCCGGCTCCGCGCAGGGCTCGGGCAAGCGGCCGCCACAGAAACAGTTTTTGCAGATCGTGCCGCG | |
| AGGTGTCATGTTCGACGGTCAGACGGGGTTGATCAAGCATAAGACGGGACGGCTGCCTCTCATGTTCTAT | |
| CGAGAGATTAAACATTTGTTGAGTCATGACATGGTTTGGCCGTGTCCTTGGCGCGAGACCCTGGTGGGTC | |
| GCGTGGTGGGACCTATTCGTTTTCACACCTACGATCAGACGGACGCCGTGCTCTTCTTCGACTCGCCCGA | |
| AAACGTGTCGCCGCGCTATCGTCAGCATCTGGTGCCTTCGGGGAACGTGTTGCGTTTCTTCGGGGCCACA | |
| GAACACGGCTACAGTATCTGCGTCAACGTTTTCGGGCAGCGCAGCTACTTTTACTGTGAGTACAGCGACA | |
| CCGATAGGCTGCGTGAGGTCATTGCCAGCGTGGGCGAACTAGTGCCCGAACCGCGGACGCCATACGCCGT | |
| GTCTGTCACGCCGGCCACCAAGACCTCCATCTATGGGTACGGGACGCGACCCGTGCCCGATTTGCAGTGT |
Started here: https://nextstrain.org/docs/getting-started/introduction
Installed on Chlamy (behind Emory VPN)
mkdir nextstrain
cd nextstrain
curl http://data.nextstrain.org/nextstrain.yml --compressed -o nextstrain.yml
conda env create -f nextstrain.yml
conda activate nextstrain
| #! /usr/bin/env nextflow | |
| import groovy.json.JsonSlurper | |
| import groovy.text.SimpleTemplateEngine | |
| import groovy.util.FileNameByRegexFinder | |
| import java.nio.file.Path | |
| import java.nio.file.Paths | |
| import nextflow.util.SysHelper | |
| PROGRAM_NAME = workflow.manifest.name | |
| VERSION = workflow.manifest.version |