johnbradley

Two Repo Problem

When working on a research project often the code is kept private until a paper is published. In conflict with this is the need to have a public repo to support some of the following needs:

• Serve a website via a ghpages branch
• Act as a placeholder for when the paper is published
• Share previous code from earlier paper

The typical approach is to have one public git repo and one private git repo.

Merging Code Problem

johnbradley

from morphosource import search_media
from functools import wraps
from time import time
import requests
from bs4 import BeautifulSoup

def timing(f):
    @wraps(f)
    def wrap(*args, **kw):
        ts = time()

johnbradley

python3 -c 'import sys; print(sys.exec_prefix + "/bin")'

johnbradley

class: Workflow
cwlVersion: v1.1
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
  str1:
    type: string
    default: "red"
  str2:

johnbradley

import re

with open("toiloutput.log") as infile:
    lines = infile.readlines()

jobs = {}

for line in lines:
    time, end = line.strip().split("  ")
    time = re.sub(r',.*', '', time)

johnbradley

{
    "$graph": [
        {
            "class": "Workflow",
            "label": "exomeseq-gatk4/v2.0.0",
            "doc": "Whole Exome Sequence analysis using GATK4 - v2.0.0",
            "requirements": [
                {
                    "class": "ScatterFeatureRequirement"
                },

johnbradley

{
    "$graph": [
        {
            "class": "Workflow",
            "label": "exomeseq-gatk3/v4.1.1",
            "doc": "Whole Exome Sequence analysis using GATK3 - v4.1.1",
            "requirements": [
                {
                    "class": "ScatterFeatureRequirement"
                },

johnbradley

{
    "$graph": [
        {
            "class": "Workflow",
            "doc": "Reverse the lines in a document, then sort those lines.",
            "requirements": [
                {
                    "class": "ScatterFeatureRequirement"
                }
            ],

johnbradley

{
    "class": "CommandLineTool",
    "inputs": [
        {
            "type": "File",
            "id": "#main/file1"
        }
    ],
    "outputs": [
        {

johnbradley

# command line program to demonstrate how to run exomeseq workflow
# against some files stored in a DukeDS project.
# Should be run within a python enviroment that has installed `bespin-cli`.
# Assumes that bespin-cli and DukeDSClient config files are already setup.

# command line program to demonstrate how to run exomeseq workflow
# against some files stored in a DukeDS project
# does not handle a read split across multiple files

from __future__ import print_function