mwalzer

{ "mzQC": {
    "creationDate": "2020-12-03T19:51:02",
    "version": "1.0.0",
    "contactName": "Mathias Walzer", 
    "contactAddress": "walzer@ebi.ac.uk", 
    "description": "This is an example of an mzQC file produced from a proteomics QC2 sample. 20 ug dried Pierce HeLa protein digest standard from Thermo Fisher Scientific (Part number: 88329) are dissolved in 200 uL of 0.1% formic acid in water to a final concentration of 100 ng/uL. A total amount of 1 uL (100ng) is injected per analysis.",
    "runQualities": [
      {
        "metadata": {
          "inputFiles": [

mwalzer

{
  "mzQC": {
    "creationDate": "2020-12-01T14:19:09",
    "contactName": "MW & CB",
    "contactAddress":  "spam@noreply.com",
    "version": "1.0.0",
    "description": "A multi-run example, where sets of runs are grouped into setQualities according to the experimental design. 
        Each setQuality has a label annotation, that must be unique. The label also lends itself as input source to axis labels 
        if you need to plot a figure from multiple setQualities. If you want to specifiy an upper level of hierarchy (summarizing 
        dimensions), then add a describing cvParameter in metadata. E.g. you have a sets, one set describes a group at a specific 

mwalzer

{ "mzQC": {
    "creationDate": "2020-12-01T11:56:34",
    "version": "1.0.0",
    "contactName": "Mathias Walzer",
    "contactAddress": "walzer@ebi.ac.uk",
    "runQualities": [
      {
        "metadata": {
          "inputFiles": [
            {

mwalzer

N.b.: before pasting into tools like http://jsonpath.herokuapp.com/ or http://www.jsonquerytool.com/ remove excess , and ..., 

...
"qualityMetrics": [
	{"cvRef": "ref_not_prefix", "accession": "QC:123", "name": "metric1", "value": 1},...
],
"controlledVocabularies": [
	{"ref": "ref_not_prefix", "name": "Proteomics Standards Initiative Quality Control Ontology", "uri": "https://github.com/HUPO-PSI/qcML-development/blob/master/cv/v0_1_0/qc-cv.obo", "version": "0.1.0"}, 
	{"ref": "MS", "name": "Proteomics Standards Initiative Mass Spectrometry Ontology", "uri": "https://github.com/HUPO-PSI/psi-ms-CV/blob/master/psi-ms.obo", "version": "4.1.7"}
]

mwalzer

import hashlib 

def sha256fromfile(filename: str) -> str:
    sha  = hashlib.sha256()
    b  = bytearray(128*1024)
    mv = memoryview(b)
    with open(filename, 'rb', buffering=0) as f:
        for n in iter(lambda : f.readinto(mv), 0):
            sha.update(mv[:n])
    return sha.hexdigest()

mwalzer

#!/usr/bin/env python
__author__ = 'walzer'
import sys
import argparse
import pyopenms as oms
import pandas as pd
from os import path

VERSION = "0.2"

mwalzer

#!/usr/bin/env python
__author__ = 'walzer'
import sys
import os
import subprocess
from datetime import datetime
import logging
import argparse
#import pickle

mwalzer

!/usr/bin/env nextflow

/*
========================================================================================
            Epiphany OpenMS workflow for protein inference
========================================================================================
 @#### Authors
 Mathias Walzer <walzer@ebi.ac.uk>
----------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------

mwalzer

{ "mzQC": {
  "creationDate": "2019-08-15T11:35:23",
  "version": "0_0_11",
  "runQualities": [
    {
      "metadata": {
        "inputFiles": [
          {
            "location": "file:///dev/null",
            "name": "CPTAC_CompRef_00_iTRAQ_01_2Feb12_Cougar_11-10-09.raw",

mwalzer

#!/bin/bash
IPT="/sbin/iptables"

# Server IP
SERVER_IP="$(ip addr show eth0 | grep 'inet ' | cut -f2 | awk '{ print $2}')"

# Your DNS servers you use: cat /etc/resolv.conf
DNS_SERVER="8.8.4.4 8.8.8.8"

# Allow connections to this package servers