Docker_tutorial.ipynb

docker_tutorial.ipynb

{
  "nbformat": 4,
  "nbformat_minor": 0,
  "metadata": {
    "colab": {
      "name": "Docker_tutorial.ipynb",
      "provenance": [],
      "toc_visible": true,
      "authorship_tag": "ABX9TyM+wkCH2mREwmKtqRqVNYk3",
      "include_colab_link": true
    },
    "kernelspec": {
      "name": "python3",
      "display_name": "Python 3"
    },
    "language_info": {
      "name": "python"
    }
  },
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "view-in-github",
        "colab_type": "text"
      },
      "source": [
        "<a href=\"https://colab.research.google.com/gist/BragatteMAS/b8e9031bcf1e7eda8b7cd5e0680fccbb/docker_tutorial.ipynb\" target=\"_parent\"><img src=\"https://colab.research.google.com/assets/colab-badge.svg\" alt=\"Open In Colab\"/></a>"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "KOlzbZkEO3c5"
      },
      "source": [
        "# Docker **Tutorial** \n",
        " \n",
        "Refactor @Bragatte 20210513\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "jKm35p3ZP0qz"
      },
      "source": [
        "    # commentaries\n",
        "    #= explanation\n",
        "    ## editable to your pc\n",
        "    #! be carefull with this moment\n",
        "\n",
        "Commands to be executed at terminal\n",
        "\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "hRG-WwIQQh9v"
      },
      "source": [
        "## Activation step-by-step Docktope\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "fTgFmc2cQMlZ"
      },
      "source": [
        "### Install\n"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "bgPVAbrqPzBF"
      },
      "source": [
        "sudo apt install docker.io\n",
        "sudo groupadd docker\n",
        "sudo usermod -aG docker bragatte #= -a = attach group"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "sgmugF-9QRjy"
      },
      "source": [
        "### Activate"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "xfnOSei8PznO"
      },
      "source": [
        "sudo systemctl start docker\n",
        "sudo systemctl enable docker"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "PfTOzYYJQBu4"
      },
      "source": [
        "### Download Docktope-image "
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "VdFC8g_YOz0I"
      },
      "source": [
        "#! Download imagem Docktope - maybe should use SUDO\n",
        "sudo docker load -i /home/bragatte/Documents/docktope-image.tar #= -i = iterative"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "5ZV5V4FrRd3i"
      },
      "source": [
        "### Start the container\n"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "4Ag3TK1MRdk6"
      },
      "source": [
        "sudo docker run docktope"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "lBuXTGMoRkVg"
      },
      "source": [
        "### Verify repository\n"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "U1w6pay9Rk5D"
      },
      "source": [
        "docker images"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "nOoeHBkXR4NF"
      },
      "source": [
        "### ##Optional"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "NpGO8rI-R4fj"
      },
      "source": [
        "##Start container locally\n",
        "docker run --rm -it docktope #= -rm = recursive memory/ it = iterative with terminal"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "1_jhE9JoSPnF"
      },
      "source": [
        "##verify repository locally - in new terminal will show the container ID\n",
        "##Just to check the container, after that came back to the first terminal\n",
        "docker ps "
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "1rppsY0ESZX5"
      },
      "source": [
        "##Leave the repository\n",
        "'exit'"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "bHPQFH28SZ-5"
      },
      "source": [
        "### Upload the directory with targets into container"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "iGz0WiK5SaQS"
      },
      "source": [
        "sudo docker run --rm -it -v /home/user/Documents/Docker:/home/test docktope\n",
        "#= -v = volumedriver(return files to local directory))\n",
        "#! attention with directories"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "hSX2pfM4Suic"
      },
      "source": [
        "### List files into container/local (/home/test)"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "oowMa5iRSuz_"
      },
      "source": [
        "ls -1v /home/test/"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "_8WBo8gaS2y5"
      },
      "source": [
        "### Script multiple\n"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "H67Tfk02S4bk"
      },
      "source": [
        "queue_docktope.sh A0201 8 teste.csv"
      ],
      "execution_count": null,
      "outputs": []
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "faw_8rpeS-ub"
      },
      "source": [
        "Script single Fasta\n",
        "\n",
        "Done!"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "knCsr9W4TCVG"
      },
      "source": [
        ""
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {
        "id": "x8TgCtm_THHx"
      },
      "source": [
        "## Activation all together Docktope\n"
      ]
    },
    {
      "cell_type": "code",
      "metadata": {
        "id": "hhRm5MlfTKxC"
      },
      "source": [
        "# commentaries\n",
        "#= explanation\n",
        "## editable to your pc\n",
        "#! be carefull with this moment\n",
        "\n",
        "#Install:\n",
        "sudo apt install docker.io\n",
        "sudo groupadd docker\n",
        "sudo usermod -aG docker bragatte #= -a = attach group\n",
        "\n",
        "-----------\n",
        "#Activate:\n",
        "1\tsudo systemctl start docker\n",
        "2\tsudo systemctl enable docker\n",
        "\n",
        "#Download Docktope-image \n",
        "\n",
        "#Download imagem Docktope - maybe should use SUDO\n",
        "3\tsudo docker load -i /home/bragatte/Documents/docktope-image.tar\n",
        "#= -i = iterative\n",
        "\n",
        "#Start the container\n",
        "sudo docker run docktope\n",
        "\n",
        "#verify repository\n",
        "docker images\n",
        "---\n",
        "##Optional\n",
        "##Start container locally:\n",
        "docker run --rm -it docktope #-rm = recursive memory/ it = iterative with terminal\n",
        "##verify repository locally - in new terminal will show the container ID\n",
        "##Just to check the container, after that came back to the first terminal\n",
        "docker ps \n",
        "##Leave the repository\n",
        "'exit'\n",
        "---\n",
        "#Upload the directory with targets into container\n",
        "4 sudo docker run --rm -it -v /home/bragatte/Documents/Docker:/home/test docktope\n",
        "#= -v = volumedriver(return files to local directory))\n",
        "#! attention with directories\n",
        "\n",
        "# List files into container/local (/home/test)\n",
        "ls -1v /home/test/\n",
        "\n",
        "# Script multiple\n",
        "6 queue_docktope.sh A0201 8 teste.csv\n",
        "\n",
        "# Script single Fasta\n",
        "# Done!"
      ],
      "execution_count": null,
      "outputs": []
    }
  ]
}