jurgjn

#!/usr/bin/env python

import argparse
import collections
import csv
import itertools
import logging
import json
import os
import uuid

jurgjn

Journal club

Moved to: https://github.com/jurgjn/jc/blob/master/SCHEDULE.md

jurgjn

#!/bin/bash

# check commands: slopBed, bedGraphToBigWig and bedClip

which bedtools &>/dev/null || { echo "bedtools not found! Download bedTools: <http://code.google.com/p/bedtools/>"; exit 1; }
which bedGraphToBigWig &>/dev/null || { echo "bedGraphToBigWig not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }
which bedClip &>/dev/null || { echo "bedClip not found! Download: <http://hgdownload.cse.ucsc.edu/admin/exe/>"; exit 1; }

# end of checking

jurgjn

#!/usr/bin/python
# Force to use (system) python2
#!/usr/bin/env python

description = """\
Usage: BaseSpaceRunDownloader_v2.py -r <ProjectName> -a <AccessToken>

This is a modified version of the BaseSpace Python Run Downloader from Illumina. It takes 
the project name (instead of the run id) and downloads base calls as fastq files (instead of
the image/intensity data).