moonwatcher

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

# Author: Lior Galanti
# email: lior.galanti@gmail.com
# Name / Country classifier
# Uses Decision Tree classifier to predict country from person name
# Decision Tree implementation: http://scikit-learn.org/stable/

import os

moonwatcher

# numpy arrays
x = np.append(x[0], np.int64(2))

# filtering ascii and accented
[^a-z:"\}\{\[\]\s,'áýéèøúạñóüæÁíÉëṭńỗœọĭãōāßķễìŠęćĐùÜỳıőếÖốğÍṇÑÚşṃţØâÿÅớệİīờịụầåłöțêÓảưǎсņēïậůžěòăşșÞðäążūÇçþǒàõąňồėļữĝûřśžŽơÂťôĽîČĎź]

moonwatcher

#!/bin/bash

CORES=8
BASECALLS="/share/140430_SN7001341_0074_AC49ANACXX/Data/Intensities/BaseCalls/"
FASTQ_BASE="/share/manual"

SAMPLE_SHEET_HEAD="FCID,Lane,SampleID,SampleRef,Index,Description,Control,Recipe,Operator,SampleProject"
BCL_TO_FASTQ_CMD="/usr/local/bin/configureBclToFastq.pl"

make_sample_sheet(){

moonwatcher

#!/bin/bash

# load modules
module load bcl2fastq/gnu/1.8.4

CORES=12
EMAIL='lg1883@nyu.edu'
BASECALLS="/scratch/gencore/manual/140617_SN911_0218_AC4G9YACXX/Data/Intensities/BaseCalls/"
FASTQ_BASE="/scratch/gencore/manual"

moonwatcher

#!/bin/sh

# NOTICE: This assumes RSA key authentiction has been set up to rsync over ssh can proceed without prompting for a password.

#PBS -V
#PBS -l nodes=1:ppn=1,walltime=48:00:00
#PBS -M lg1883@nyu.edu
#PBS -m abe
#PBS -q s48
#PBS -l mem=1GB

moonwatcher

#!/bin/bash
SOURCE="$1"
TARGET="$2"
NAME="$3"
EMAIL="eegi"

LOG_DIR="/var/log/scope/$NAME";
FILTER_FILE="/var/lib/scope/filter/$NAME"
TIMESTAMP="$(date +%Y-%m-%d-%H-%M-%S)";
CHMOD="a+rwx,g+rwx,o-w"

moonwatcher

#!/bin/bash

# load modules
module load bcl2fastq/gnu/1.8.4

CORES=12
EMAIL='lg1883@nyu.edu'
BASECALLS="/scratch/gencore/manual/140617_M02455_0020_000000000-A9GDG/Data/Intensities/BaseCalls/"
FASTQ_BASE="/scratch/gencore/manual"

moonwatcher

#!/bin/bash
 
# load modules
# module load bcl2fastq/gnu/1.8.4
 
CORES=12
EMAIL='lg1883@nyu.edu'
BASECALLS="/scratch/gencore/manual/140703_M02455_0021_000000000-A8P38/Data/Intensities/BaseCalls/"
FASTQ_BASE="/scratch/gencore/manual"
 

moonwatcher

#!/bin/bash

# load modules
# module unload bcl2fastq/gnu/1.8.4
# module load bcl2fastq/gnu/1.8.4

CORES=12
EMAIL='lg1883@nyu.edu'
BASECALLS="/scratch/gencore/hiseq-700911/140617_SN911_0218_AC4G9YACXX/Data/Intensities/BaseCalls/"
FASTQ_BASE="/scratch/gencore/manual"

moonwatcher

#!/bin/bash

NAME="C4W17ACXX"
EMAIL='lg1883@nyu.edu'

FLOWCELL_PATH="/scratch/gencore/hiseq-700911/140710_SN911_0221_AC4W17ACXX"
OUTPUT_PATH="/scratch/gencore/manual/140710_SN911_0221_AC4W17ACXX"

CONFIGURE_BCL2FASTQ="\
--fastq-cluster-count 0 \