moonwatcher

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
    <dict>
        <key>Label</key>
        <string>edu.nyu.bio.tuboweb</string>
        
        <key>WorkingDirectory</key>
        <string>/Users/gs/DEV/gencore</string>
        

moonwatcher

{
    "name": "HABDFADXX",
    "email": "lg1883@nyu.edu",
    "flowcell path": "/export/data1/gencore/140918_SN911_0232_BHABDFADXX",
    "output path": "/export/data1/demux",
    "configure bcl2fastq": "",
    "sample sheet": [
        "HABDFADXX,1,SV51,,CGATGT,,N,,,lane1",
        "HABDFADXX,1,SV52,,TGACCA,,N,,,lane1",
        "HABDFADXX,1,SV53,,ACAGTG,,N,,,lane1",

moonwatcher

{
    "name": "C51F4ACXX",
    "email": "lg1883@nyu.edu",
    "flowcell path": "/export/data1/gencore/140911_SN911_0231_BC51F4ACXX",
    "output path": "/export/data1/demux",
    "configure bcl2fastq": "",
    "sample sheet": [
        "C51F4ACXX,2,ANUT_12_01,,TGACCA,,N,,,lane2",
        "C51F4ACXX,2,ANUT_12_02,,ACAGTG,,N,,,lane2",
        "C51F4ACXX,2,ANTT_12_01,,GCCAAT,,N,,,lane2",

moonwatcher

{
    "name": "000000000-AAK03",
    "email": "lg1883@nyu.edu",
    "flowcell path": "/export/data1/gencore/140911_M02455_0025_000000000-AAK03",
    "output path": "/export/data1/demux",
    "configure bcl2fastq": "",
    "sample sheet": [
        "000000000-AAK03,1,pBOB11_1,,GTTTCG,,N,,,lane1",
        "000000000-AAK03,1,pBOB11_3,,CGTACG,,N,,,lane1",
        "000000000-AAK03,1,pBOB11_5a,,GAGTGG,,N,,,lane1",

moonwatcher

{
    "name": "C4MVUACXX_dual",
    "email": "lg1883@nyu.edu",
    "flowcell path": "/export/data1/gencore/140828_SN911_0230_AC4MVUACXX",
    "output path": "/export/data1/demux",
    "configure bcl2fastq": "--use-bases-mask \"Y*,I8n,I8n,Y*\" --tiles \"s_6\"",
    "sample sheet": [
        "C4MVUACXX,6,G140_A6_L1,,TAGATCGC-TAAGGCGA,,N,,,lane6",
        "C4MVUACXX,6,G140_A6_L114,,TAGATCGC-CGTACTAG,,N,,,lane6",
        "C4MVUACXX,6,G140_A6_L115,,TAGATCGC-AGGCAGAA,,N,,,lane6",

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",

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": "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": "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

#!/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 \