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| @@ -0,0 +1,47 @@ | ||
| ############################################################################### | ||
| # | ||
| # Software to be installed in the main environment | ||
| # | ||
| # AUTHOR: Maciej_Bak | ||
| # CONTACT: wsciekly.maciek@gmail.com | ||
| # CREATED: 15-02-2022 | ||
| # LICENSE: Apache_2.0 | ||
| # | ||
| ############################################################################### | ||
| --- | ||
|
|
||
| name: warlock | ||
|
|
||
| channels: | ||
| - conda-forge | ||
| - bioconda | ||
|
|
||
| dependencies: | ||
| - bioconductor-graph>=1.76.0 | ||
| - bioconductor-rgraphviz>=2.42.0 | ||
| - boost-cpp>=1.74.0 | ||
| - compilers>=1.7.0 | ||
| - graphviz>=8.0.3 | ||
| - jinja2>=3.1.2 | ||
| - python>=3.8.0 | ||
| - pyyaml>=6.0 | ||
| - r-ape>=5.8 | ||
| - r-base>=4.0.3 | ||
| - r-data.table>=1.15.4 | ||
| - r-devtools>=2.4.5 | ||
| - r-dplyr>=0.7.0 | ||
| - r-ggmuller>=0.5.6 | ||
| - r-ggplot2>=3.5.1 | ||
| - r-gridextra>=2.3 | ||
| - r-lazyeval>=0.2.2 | ||
| - r-moments>=0.14.1 | ||
| - r-optparse>=1.7.5 | ||
| - r-rcolorbrewer>=1.1_3 | ||
| - r-readr>=2.1.5 | ||
| - r-rlang>=1.1.4 | ||
| - r-rvaidememoire>=0.9_83_7 | ||
| - r-scales>=1.3.0 | ||
| - r-teachingdemos>=2.12.1 | ||
| - snakemake>=7.18.2 | ||
|
|
||
| ... |
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| #!/bin/bash | ||
|
|
||
| set -ex | ||
| Rscript -e "devtools::install_github('robjohnnoble/demonanalysis', upgrade=FALSE)" |
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| { | ||
| "cells": [ | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "1928a2a5", | ||
| "metadata": { | ||
| "tags": [] | ||
| }, | ||
| "source": [ | ||
| "### _warlock_ vignette" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "4450695b", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "The following notebook demonstrates workflow execution with a simple set of simulation parameters." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "89b9ced8", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "import os\n", | ||
| "from IPython.display import Image" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "0a4b57d1", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Prepare files for the workflow" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "9f7ed01b", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "In the example below we will prepare a configuration file varying one specific parameter: deme carrying capacity.\n", | ||
| "\n", | ||
| "All dependencies have been already installed while building a container for this notebook." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "63403efe", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Compile _demon_ (skip this step unless you use MyBinder service for notebook exploration)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "90a4c46c", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "%%bash\n", | ||
| "\n", | ||
| "g++ resources/demon_model/src/demon.cpp -o resources/demon_model/bin/demon -I/srv/conda/envs/notebook/include/ -lm" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "cb706573", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "Prepare configfile for the workflow (based on a template)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "3aa3277f", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "with open(\"tests/binder/config-template.yml\") as f:\n", | ||
| " configlines = f.read().splitlines()\n", | ||
| "\n", | ||
| "configlines[17] = \"workflow_repo_path: \\\"\" + os.getcwd() + \"\\\"\"\n", | ||
| "\n", | ||
| "outdir = os.path.join(\n", | ||
| " os.getcwd(),\n", | ||
| " \"tests\",\n", | ||
| " \"binder\",\n", | ||
| " \"output\"\n", | ||
| ")\n", | ||
| "\n", | ||
| "configlines[22] = \"workflow_analysis_outdir: \\\"\" + outdir + \"\\\"\"\n", | ||
| "\n", | ||
| "with open(\"tests/binder/config.yml\", \"w\") as f:\n", | ||
| " for line in configlines:\n", | ||
| " f.write(line + os.linesep)" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "5298889a", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Execute the workflow" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "59834894", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "We trigger the snakemake workflow via our main bash script (~5min runtime)." | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "6f9a1e6a", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "%%bash\n", | ||
| "\n", | ||
| "time \\\n", | ||
| "bash warlock.sh \\\n", | ||
| "--configfile tests/binder/config.yml \\\n", | ||
| "--environment local \\\n", | ||
| "--cores 3" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "7317904e", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "## Inspect summary plots:" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "01c72cb9", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "$\\log_2$[deme carrying capacity] = 8" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "2b0f8217", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "Image(filename=\"tests/binder/output/analyses/00000000/muller.png\") " | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "518dde2c", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "$\\log_2$[deme carrying capacity] = 9" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "0e4a74b6", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "Image(filename=\"tests/binder/output/analyses/00000001/muller.png\") " | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "123529a1", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "$\\log_2$[deme carrying capacity] = 10" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "code", | ||
| "execution_count": null, | ||
| "id": "018e1056", | ||
| "metadata": {}, | ||
| "outputs": [], | ||
| "source": [ | ||
| "Image(filename=\"tests/binder/output/analyses/00000002/muller.png\") " | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "dfdd7551", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "**The simple example above highlights that the higher the deme carrying capacity is the easier the tumor evolves within the population.**" | ||
| ] | ||
| }, | ||
| { | ||
| "cell_type": "markdown", | ||
| "id": "782ed072", | ||
| "metadata": {}, | ||
| "source": [ | ||
| "---" | ||
| ] | ||
| } | ||
| ], | ||
| "metadata": { | ||
| "kernelspec": { | ||
| "display_name": "Python 3 (ipykernel)", | ||
| "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": "3.11.0" | ||
| } | ||
| }, | ||
| "nbformat": 4, | ||
| "nbformat_minor": 5 | ||
| } |