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#!/usr/bin/env python

import os
import sys
import subprocess
import time
import logging
import ipyparallel

TEMPLATE="""#!/bin/sh

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1064,1068d1063
<                 retries = 0
<                 while not os.path.isfile(file_or_archive):
<                     time.sleep(5)
<                     if retries > 5: break
<                     retries += 1
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<                 retries = 0
<                 while not os.path.isfile(file_or_archive):
<                     time.sleep(5)

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c = get_config()
### If you want to auto-save .html and .py versions of your notebook:
# modified from: https://github.com/ipython/ipython/issues/8009
import os
from subprocess import check_call

def post_save(model, os_path, contents_manager):
    """post-save hook for converting notebooks to .py scripts"""
    if model['type'] != 'notebook':
        return # only do this for notebooks

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#!/bin/bash
# Trying to get biopython to parse SRA xml output. I think I need these XSDs produced by SRA to do this.

if [ ! -e ~/.biopython/Bio/Entrez/XSDs ]; then mkdir -p ~/.biopython/Bio/Entrez/XSDs; fi
cd ~/.biopython/Bio/Entrez/XSDs

wget -O SRA.common.xsd "http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.common.xsd?view=co"
wget -O SRA.submission.xsd "http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.submission.xsd?view=co"
wget -O SRA.study.xsd "http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.study.xsd?view=co"
wget -O SRA.sample.xsd "http://www.ncbi.nlm.nih.gov/viewvc/v1/trunk/sra/doc/SRA_1-5/SRA.sample.xsd?view=co"

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from pprint import pprint
import jinja2
import markdown

HTML_TEMPLATE = """{% macro get_html() %}
{{ content | markdown }}
{% endmacro %}
{% set html_content = get_html() %}

Title from Markdown meta-data: {{ get_title() }}

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#!/bin/bash
# This is a little bash script to create a tunnel for running jupyter
# notebooks.
#
# You can run the script like so:
#
#   $ jupyterTunnel start remote1
#
# This will create an ssh tunnel on port 7000 to remote 1, and create a control
# socket 'jupyter-ctrl-socket' in the current working direcotry. To stop the

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# see https://www.topbug.net/blog/2013/04/14/install-and-use-gnu-command-line-tools-in-mac-os-x/

# core
brew install coreutils

# key commands
brew install binutils
brew install diffutils
brew install ed --default-names
brew install findutils --with-default-names

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@namespace url(http://www.w3.org/1999/xhtml);
/* minimal page background */
  #pageContainer {
   margin-top: 24px;
  }
  .page {
    max-width: 100% !important;
    border: none !important;
    margin-bottom: 0 !important;
    /* fix for dynamic positioning of the .page div */

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# vim: set ft=snakemake:
shell.prefix("""set -euo pipefail;
             if [ -e /lscratch/$SLURM_JOBID ]; then
                 export TMPDIR=/lscratch/$SLURM_JOBID
             else
                 export TMPDIR=/tmp
             fi;
             """)
workdir: '.'

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#/usr/bin/env python
import os

from lcdblib.snakemake import helpers
from lcdblib.utils import utils

URI = '../lcdb-wrapper-tests'
TMPDIR='/mnt/threeTB/centos_scratch'
references = {
    'dmel': {