pvanheus

pvanheus

#!/bin/sh

# requirement:
# working directory with:
# in/ - files named .fasta that are query sequences
# out/ - empty directory to put outputs in
# logs/ - empty directory to put logs in 
#
# qsub with:
# qsub -t 1-2 -wd ./my-work-dir blastplus_array.sh

pvanheus

#!/usr/bin/python

from Bio import SeqIO
import argparse
import sys

parser = argparse.ArgumentParser(description='Split a FASTA file into a number of chunks')
parser.add_argument('input_file', type=file, help='Input FASTA file')
parser.add_argument('output_prefix', help='Prefix of output files')
parser.add_argument('num_chunks', type=int, help='Number of chunks to split into')

pvanheus

FROM ubuntu:latest

MAINTAINER Peter van Heusden <pvh@sanbi.ac.za> version: 0.1

RUN apt-get update && apt-get install -y libmysqlclient-dev libmemcache-dev zlib1g-dev libssl-dev python-dev libxml2-dev libxslt1-dev build-essential git python-virtualenv && apt-get clean && rm -rf /var/lib/apt/lists/*

ENV JMS_USER jms
ENV JMS_USER_HOME /home/jms
ENV JMS_ROOT ${JMS_USER_HOME}/JMS
ENV JMS_SRC ${JMS_ROOT}/src

pvanheus

class pendingObject(object):

  def __init__(self, obj, contentID, type):
    self.obj = obj
    self.contentID = contentID
    self.type = type

class pendingObjectContainer(object):
  def __init__(self):
    self.data = dict()

pvanheus

#!/bin/bash

if [ $# -ge 1 ] ; then
  STEP=$#
else
  STEP=1
fi

if [ $# -ge 2 ] ; then
  MODE=$2

pvanheus

#! /bin/sh
### BEGIN INIT INFO
# Provides:          supervisord
# Required-Start:    $local_fs $remote_fs $networking
# Required-Stop:     $local_fs $remote_fs $networking
# Default-Start:     2 3 4 5
# Default-Stop:      0 1 6
# Short-Description: Starts supervisord - see http://supervisord.org
# Description:       Starts and stops supervisord as needed - see http://supervisord.org
### END INIT INFO

pvanheus

#!/bin/bash

### BEGIN INIT INFO
# Provides:             galaxy
# Required-Start:       $network $local_fs $mysql $supervisord
# Required-Stop:
# Default-Start:        2 3 4 5
# Default-Stop:         0 1 6
# Short-Description:    Galaxy
### END INIT INFO

pvanheus

#!/bin/bash

# default headphone volume (40000 is 40%)
DEFAULT_HEADPHONE_VOLUME=${DEFAULT_HEADPHONE_VOLUME-40000}
# default microphone volume (80000 is 80%)
DEFAULT_MICROPHONE_VOLUME=${DEFAULT_MICROPHONE_VOLUME-80000}
# enable headphone
ENABLE_USB_HEADPHONE=${ENABLE_USB_HEADPHONE-1}
# enable microphone
ENABLE_USB_MICROPHONE=${ENABLE_USB_MICROPHONE-0}

pvanheus

MATCH (s:Strand {forward: True}) -[:CONTAINS]->(l1:Location)
WHERE l1.end >= 1000
WITH l1
ORDER BY l1.end ASC LIMIT 1
MATCH (l1)-[:NEXT*]->(l2)
WHERE l2.start <= 7000
WITH l1,l2
ORDER BY l2.end DESC LIMIT 1
MATCH p=(l1)-[:NEXT*]->(l2)
UNWIND nodes(p) as x