rpetit3

#! /bin/bash

if [[ $# == 0 ]]; then
    echo ""
    echo "create-user NEW_USERNAME"
    echo ""
    echo "Example Command"
    echo "create-user robert_petit"
    echo ""
    exit

rpetit3

#! /bin/bash

if [[ $# == 0 ]]; then
    echo ""
    echo "reset-password NEW_USERNAME"
    echo ""
    echo "Example Command"
    echo "reset-password robert_petit"
    echo ""
    exit

rpetit3

#! /bin/bash

if [[ $# == 0 ]]; then
    echo ""
    echo "create-admin NEW_USERNAME"
    echo ""
    echo "Example Command"
    echo "create-admin robert_petit"
    echo ""
    exit

rpetit3

3d-dna
3seq
actc
aeon
agc
agouti
alcor
alignoth
ampligone
anansescanpy

rpetit3

#!/usr/bin/env python
"""
A simple script to query API to get public/private status of all repos under a namespace.

Caveat being, without an API key, you will only ever see the public repos.
"""
PROGRAM = 'quay-namespace-info'
VERSION = '1.0.0'
QUAY_API_URL= 'https://quay.io/api/v1/repository'

rpetit3

/*
This file includes default values for Teton.
*/

process {
  executor = 'slurm'
  queue = 'teton,moran'
  scratch = params.slurm_use_scratch
  time = 60.m
  clusterOptions = '--account healthdatasci'

rpetit3

#!/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

rpetit3

#! /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

rpetit3

#! /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

rpetit3

#! /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"