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   "source": [
    "### Running in Docker container on Ostrich\n",
    "\n",
    "#### Started Docker container with the following command:\n",
    "\n",
    "```docker run -p 8888:8888 -v /Users/sam/data/:/data -v /Users/sam/owl_home/:/owl_home -v /Users/sam/owl_web/:/owl_web -v /Users/sam/gitrepos:/gitrepos -it f99537d7e06a```\n",
    "\n",
    "The command allows access to Jupyter Notebook over port 8888 and makes my Jupyter Notebook GitHub repo and my data files on Owl/home and Owl/web accessible to the Docker container.\n",
    "\n",
    "Once the container was started, started Jupyter Notebook with the following command inside the Docker container:\n",
    "\n",
    "```jupyter notebook```\n",
    "\n",
    "This is configured in the Docker container to launch a Jupyter Notebook without a browser on port 8888.\n",
    "\n",
    "The Docker container is running on an image created from this [Dockerfile (Git commit 443bc42)](https://github.com/sr320/LabDocs/blob/443bc425cd36d23a07cf12625f38b7e3a397b9be/code/dockerfiles/Dockerfile.bio)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "date"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Check computer specs"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "hostname"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "lscpu"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Download all <em>Ostrea lurida</em> files from BGI using ```wget```"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### This uses the ```-m``` flag to recursively download all files and mirror the directory structure of the target. Additionally, it uses the ```-P``` flag to specify the output location of the downloaded files."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "time wget -m ftp://F15FTSUSAT0327:OSTibkD@cdts-hk.genomics.cn/Ostrea_lurida/ \\\n",
    "- P /owl_web/O_lurida_genome_assemblies_BGI/20161201/"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Noticed that the files weren't being saved in the specified directory..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "ls /owl_web/O_lurida_genome_assemblies_BGI/20161201/"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Instead, they were being saved in my current directory..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "ls -l cdts-hk.genomics.cn/"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Not going to waste time figuring out why the ```-P``` argument didn't work for ```wget```, so just changing to desired directory and running ```wget``` command again..."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "cd /owl_web/O_lurida_genome_assemblies_BGI/20161201/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "pwd"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Well, that's weird... Try again without bash magics?"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "cd /owl_web/O_lurida_genome_assemblies_BGI/20161201/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "time wget -m ftp://F15FTSUSAT0327:OSTibkD@cdts-hk.genomics.cn/Ostrea_lurida/"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### View directory structure of downloaded files\n",
    "\n",
    "Note: The following program (```tree```) was installed via [Homebrew package manager](http://brew.sh/)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "tree /owl_web/O_lurida_genome_assemblies_BGI/20161201/"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Download all <em>Panopea gererosa</em> files from BGI using ```wget```"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "cd /owl_web/P_generosa_genome_assemblies_BGI/20161201/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "time wget -m ftp://F15FTSUSAT0327:OSTibkD@cdts-hk.genomics.cn/Panopea_generosa"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### View directory structure of downloaded files"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "%%bash\n",
    "tree /owl_web/P_generosa_genome_assemblies_BGI/20161201/"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
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