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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() |
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python3 -c 'import sys; print(sys.exec_prefix + "/bin")' |
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class: Workflow | |
cwlVersion: v1.1 | |
requirements: | |
- class: SubworkflowFeatureRequirement | |
- class: MultipleInputFeatureRequirement | |
inputs: | |
str1: | |
type: string | |
default: "red" | |
str2: |
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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) |
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{ | |
"$graph": [ | |
{ | |
"class": "Workflow", | |
"label": "exomeseq-gatk4/v2.0.0", | |
"doc": "Whole Exome Sequence analysis using GATK4 - v2.0.0", | |
"requirements": [ | |
{ | |
"class": "ScatterFeatureRequirement" | |
}, |
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{ | |
"$graph": [ | |
{ | |
"class": "Workflow", | |
"label": "exomeseq-gatk3/v4.1.1", | |
"doc": "Whole Exome Sequence analysis using GATK3 - v4.1.1", | |
"requirements": [ | |
{ | |
"class": "ScatterFeatureRequirement" | |
}, |
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{ | |
"$graph": [ | |
{ | |
"class": "Workflow", | |
"doc": "Reverse the lines in a document, then sort those lines.", | |
"requirements": [ | |
{ | |
"class": "ScatterFeatureRequirement" | |
} | |
], |
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{ | |
"class": "CommandLineTool", | |
"inputs": [ | |
{ | |
"type": "File", | |
"id": "#main/file1" | |
} | |
], | |
"outputs": [ | |
{ |
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# 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 |
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#!/bin/bash | |
set -e | |
TOKEN=TODO | |
DDS_USER_CREDENTIAL=TODO | |
QUESTIONNAIRE=TODO | |
PROJECT_ID=TODO | |
BARCODE_FILE_ID=TODO | |
SEQUENCES_FILE_ID=TODO |
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