pipeline.py

import os
import re
from ruffus import *
import subprocess
import sqlite3

parser = cmdline.get_argparse(description='Midlands-1 analysis pipeline')

parser.add_argument("-s", "--sqlite_db", type=str, help="Name and path of SQLite3 database")
parser.add_argument("-c", "--sql_command", type=str, help="SQL command to return rows")

nathanhaigh

#!/bin/bash
# Usage: deinterleave_fastq.sh < interleaved.fastq f.fastq r.fastq [compress]
# 
# Deinterleaves a FASTQ file of paired reads into two FASTQ
# files specified on the command line. Optionally GZip compresses the output
# FASTQ files using pigz if the 3rd command line argument is the word "compress"
# 
# Can deinterleave 100 million paired reads (200 million total
# reads; a 43Gbyte file), in memory (/dev/shm), in 4m15s (255s)
# 

inutano

#!/bin/zsh
#
# time file transfer from NCBI, EBI, and DDBJ with various transfer protocol.
# calc avg time send it to stdout
# usage: transfer_speed.sh <target SRA Run ID>
# requirement: SRA_Accessions.tab from ftp.ncbi.nlm.nih.gov/sra/reports/Metadata
#
###################################################################################

# time format (set as showing total time by second only)