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Merge pull request #11 from bio-tools/dev
push v0.3.0 to master and pypi
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,263 @@ | ||
| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "# Protocol of experiments 01.06.2017" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "__Goals:__\n", | ||
| " 1. Try out the proposed pipeline (see google slides)\n", | ||
| " 1. Send file back to today from future." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "__Requirements:__\n", | ||
| "1. Installed [Docker](https://store.docker.com/search?type=edition&offering=community) with the internet access\n", | ||
| "1. Python3, pip\n", | ||
| "1. Installed dependencies from requirements.txt \n", | ||
| "1. Archive of the [Integron_Finder](https://github.com/gem-pasteur/Integron_Finder/archive/master.zip)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Again, we import the Container class from docker_wrapper module." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": true | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import os" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "exec(open('../tooldog/analyse/container.py').read())" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "As in previous experiment we will define some useful constants and util functions for later use." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": true | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "def write_to_file(filename, string = ''):\n", | ||
| " \"\"\"Write string to file\n", | ||
| "\n", | ||
| " :param str filename: Filename\n", | ||
| " :param str string: String to write\n", | ||
| " \"\"\"\n", | ||
| " f = open(filename, 'w')\n", | ||
| " f.write(string)\n", | ||
| " f.close()" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": true | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "PYTHON_VERSION = 2 # version of python tool" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": true | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "TOOL_NAME = 'gem-pasteur-Integron_Finder-4d54052' # name of the tool, assuming it is available via PyPi" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": true | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "OUTPUT_FORMAT = 'cwl' # output: cwl / xml" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": true | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "OUTPUT_FILENAME = TOOL_NAME + \".\" + OUTPUT_FORMAT # output filename" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": true | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "PYTHON_PATH = \"/usr/local/lib/python3.5/dist-packages/\" if PYTHON_VERSION == 3 else \\\n", | ||
| "\"/usr/local/lib/python2.7/dist-packages/\" # PYTHONPATH, required for argparse2tool" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "CURRENT_PATH = os.path.realpath(os.getcwd())" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Now we are ready to create a container." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "c = Container(\"inkuzm/tooldog-analyser-sandbox\",\n", | ||
| " \"tail -f /dev/null\", # run until we will stop the container\n", | ||
| " environment={'PYTHONPATH': PYTHON_PATH})" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Put tarball inside the container. For this we will:\n", | ||
| " * Download tarball https://api.github.com/repos/gem-pasteur/Integron_Finder/tarball" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "c.put(CURRENT_PATH + \"/tool.tar\", \"/\")" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Let's create an executional context and a helper to execute the commands in it." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": { | ||
| "collapsed": true | ||
| }, | ||
| "outputs": [], | ||
| "source": [ | ||
| "WORKDIR = \"/\" + TOOL_NAME" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "def cd(path, cmd):\n", | ||
| " return \"bash -c 'cd \" + path + \" && \" + cmd + \"'\"" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Let's do it!" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "cwl_tool = '' \n", | ||
| "with c:\n", | ||
| " exe1 = c.exec(cd(WORKDIR, \"pip2 install .\"))\n", | ||
| " for line in exe1:\n", | ||
| " print(line)\n", | ||
| " \n", | ||
| " exe2 = c.exec(cd(WORKDIR, \"pip2 install argparse2tool\"))\n", | ||
| " for line in exe2:\n", | ||
| " print(line)\n", | ||
| " \n", | ||
| " exe3 = c.exec(cd(WORKDIR, 'integron_finder --generate_cwl_tool')) # TODO: find a way to get the toolname\n", | ||
| " for line in exe3:\n", | ||
| " cwl_tool += line.decode(\"utf-8\")[:-1]\n", | ||
| " \n", | ||
| " write_to_file(OUTPUT_FILENAME, cwl_tool)" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3", | ||
| "language": "python", | ||
| "name": "python3" | ||
| }, | ||
| "language_info": { | ||
| "codemirror_mode": { | ||
| "name": "ipython", | ||
| "version": 3 | ||
| }, | ||
| "file_extension": ".py", | ||
| "mimetype": "text/x-python", | ||
| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.6.0" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 1 | ||
| } |
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