moonwatcher

{
    "name": "C48L7ACXX_V2",
    "email": "lg1883@nyu.edu",
    "flowcell path": "/scratch/gencore/hiseq-700911/140711_SN911_0222_BC48L7ACXX",
    "output path": "/data/cgsb/gencore/manual",
    "configure bcl2fastq": "--use-bases-mask \"Y*,I6nnn,n*,Y*\" --tiles \"s_2,s_3,s_4,s_6,s_7,s_8\"",
    "sample sheet": [
        "C48L7ACXX,2,1L22A,,ATCACG,,N,,karen_hicks,lane2",
        "C48L7ACXX,2,3L22A,,CGATGT,,N,,karen_hicks,lane2",
        "C48L7ACXX,2,13L22A,,TTAGGC,,N,,karen_hicks,lane2",

moonwatcher

{
    "name": "C48L7ACXX_5",
    "email": "lg1883@nyu.edu",
    "flowcell path": "/scratch/gencore/hiseq-700911/140711_SN911_0222_BC48L7ACXX",
    "output path": "/data/cgsb/gencore/manual",
    "configure bcl2fastq": "--use-bases-mask \"Y*,I8n,I8n,Y*\" --tiles \"s_5\"",
    "sample sheet": [
        "C48L7ACXX,5,Undetermined,,Undetermined,,N,,Wei Yuan,lane5",
        "C48L7ACXX,5,Nextera-97,,TAAGGCGA-TAGATCGC,,N,,Wei Yuan,lane5",
        "C48L7ACXX,5,Nextera-98,,TAAGGCGA-CTCTCTAT,,N,,Wei Yuan,lane5",

moonwatcher

#!/usr/bin/env python
# -*- coding: utf-8 -*-

from __future__ import print_function

import sys
import os
import re
import json

moonwatcher

{
    "name": "C4RNWACXX",
    "email": "lg1883@nyu.edu",
    "flowcell path": "/media/demux/140729_SN911_0225_AC4RNWACXX",
    "output path": "/media/demux/manual",
    "configure bcl2fastq": "",
    "sample sheet": [
        "C4RNWACXX,2,140701_JD_C_1,,ACAGTG,,N,,jordane_dimidschstein,lane2",
        "C4RNWACXX,2,140701_JD_C_13,,TAGCTT,,N,,jordane_dimidschstein,lane2",
        "C4RNWACXX,2,140701_JD_C_5,,CTTGTA,,N,,jordane_dimidschstein,lane2",

moonwatcher

{
    "name": "C4MBGACXX",
    "email": "lg1883@nyu.edu",
    "flowcell path": "/media/demux/140729_SN911_0226_BC4MBGACXX",
    "output path": "/media/demux/manual",
    "configure bcl2fastq": "",
    "sample sheet": [
        "C4MBGACXX,2,140701_JD_B_10,,GATCAG,,N,,jordane_dimidschstein,lane2",
        "C4MBGACXX,2,140701_JD_B_12,,GGCTAC,,N,,jordane_dimidschstein,lane2",
        "C4MBGACXX,2,140701_JD_D_2,,ATCACG,,N,,jordane_dimidschstein,lane2",

moonwatcher

#!/bin/sh
# Protocol for setting up an environemnt for bcl2fastq 1.8.4
# See: http://seqanswers.com/forums/showpost.php?p=141026&postcount=29
# lior.galanti@nyu.edu
# for bcl2fastq2 see http://backwardincompatible.com/post/169360794395/compiling-illumina-bcl2fastq-220-on-ubuntu-with

# On Ubuntu
sudo apt-get install \
libexpat1-dev \
libexpat1 \

moonwatcher

{
    "name": "H9KMLADXX",
    "email": "lg1883@nyu.edu",
    "flowcell path": "/media/demux/140805_SN911_0227_AH9KMLADXX",
    "output path": "/media/demux/manual",
    "configure bcl2fastq": "",
    "sample sheet": [
        "H9KMLADXX,1,SV31,,CGATGT,,N,,,lane1",
        "H9KMLADXX,1,SV32,,TGACCA,,N,,,lane1",
        "H9KMLADXX,1,SV33,,ACAGTG,,N,,,lane1",

moonwatcher

{
    "name": "HA430ADXX",
    "email": "lg1883@nyu.edu",
    "flowcell path": "/export/data1/flowcell/140812_SN911_0228_AHA430ADXX",
    "output path": "/export/data1/demux",
    "configure bcl2fastq": "",
    "sample sheet": [
        "HA430ADXX,1,MRP11,,ATGTCA,,N,,,lane1",
        "HA430ADXX,1,MRP12,,CCGTCC,,N,,,lane1",
        "HA430ADXX,1,MRP13,,GTAGAG,,N,,,lane1",

moonwatcher

{
    "name": "HAAULADXX",
    "email": "lg1883@nyu.edu",
    "flowcell path": "/export/data1/flowcell/140812_SN911_0229_BHAAULADXX",
    "output path": "/export/data1/demux",
    "configure bcl2fastq": "",
    "sample sheet": [
        "HAAULADXX,1,brugia_1,,ATCACG,,N,,,lane1",
        "HAAULADXX,1,brugia_2,,CGATGT,,N,,,lane1",
        "HAAULADXX,1,brugia_4,,TTAGGC,,N,,,lane1",

moonwatcher

{
    "name": "C4MVUACXX_single",
    "email": "lg1883@nyu.edu",
    "flowcell path": "/export/data1/gencore/140828_SN911_0230_AC4MVUACXX",
    "output path": "/export/data1/demux",
    "configure bcl2fastq": "--use-bases-mask \"Y*,I6nnn,n*,Y*\" --tiles \"s_2,s_3,s_4,s_5,s_7,s_8\"",
    "sample sheet": [
        "C4MVUACXX,2,SDW_G3_1,,ACAGTG,,N,,,lane2",
        "C4MVUACXX,2,SDW_GOR69_1,,CGATGT,,N,,,lane2",
        "C4MVUACXX,2,SDW_NYCG3_1,,GCCAAT,,N,,,lane2",