Alternative approaches [click to expand]

\n\n1. While it is better to leave the code within the volume for better performance you may wish to use another [bind mount](https://docs.docker.com/storage/bind-mounts/) to overlay the volume's `~/src` folder with a host directory containing the Chaste source code e.g. `-v /path/to/chaste_code:/home/chaste/src`. Chaste may then need to be recompiled within the container with `build_chaste.sh ` or if you already have the code in the mounted host folder, cloning can be skipped before recompiling with `build_chaste.sh .`. This will make the same source files directly accessible on both the host and within the Docker container, avoiding the need to copy files back and forth or use VS Code. This may result in slower I/O than when stored in a Docker volume, however this problem may be ameliorated on [macOS](https://docs.docker.com/storage/bind-mounts/#configure-mount-consistency-for-macos) with the [`delegated` option](https://docs.docker.com/docker-for-mac/osxfs-caching/#examples) e.g. `--mount type=bind,source=\"$(pwd)\"/chaste_code,destination=/home/chaste/src,consistency=delegated`.\n\n2. Alternatively, use the utility `docker-sync`: http://docker-sync.io/. This works on OSX, Windows, Linux (where it maps on to a native mount) and FreeBSD.\n

\n\n> :information_source: For small edits to the code from the terminal, `nano` is installed in the image for convenience, along with `git` for pushing the changes.\n\nInstalling additional software\n------------------------------\n\nIf you want to use a package which is not installed within the image, you can install it with the command:\n\n```\nsudo apt-get update && sudo apt-get install \n```\nReplacing `` as appropriate. Enter the password: `chaste` when prompted to do so.\n\nNote that packages installed this way will not persist after the container is deleted (because the relevant files are not stored in `/home/chaste`). This can be avoided by omitting the `--rm` flag from the `docker run` command and using `docker start ` to relaunch a previously used container. If there is a package you think would be a particularly useful permanent addition to the Docker image, then email your suggestion to me or submit a pull request.\n\nTesting\n-------\n\nTo check Chaste compiled correctly you may wish to [run the continuous test pack](https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides/CmakeFirstRun#Testingstep) from the `CHASTE_BUILD_DIR` directory:\n```\nctest -j$(nproc) -L Continuous\n```\nThe script `test.sh` (in `/home/chaste/scripts`) is provided in the users's path for convenience.\n\nThe following test can be run separately to quickly check the build environment and installed dependencies available to chaste:\n```\nctest --verbose -R TestChasteBuildInfo$\n```\nFor more information on testing see: https://chaste.cs.ox.ac.uk/trac/wiki/ChasteGuides/CmakeBuildGuide. \n\n## Advanced usage\n### Building your own image\nIf you're a more advanced developer and want to build your own image with a particular code branch, make sure you have Docker up and running then read on! In these examples, we tag the image `chaste:custom` for illustration but you are encouraged to give it a more descriptive name.\n\n1. Build the Chaste image:\n 1. From the latest commit on Chaste's GitHub `develop` branch:\n ```\n docker build -t chaste:custom --build-arg GIT_TAG=develop https://github.com/chaste/chaste-docker.git\n ```\n 2. Alternatively a specific branch or tag may be specified through the argument `--build-arg GIT_TAG=` (with the same tag appended onto the docker image name for clarity) e.g.:\n ```\n docker build -t chaste:custom --build-arg GIT_TAG=2024.1 https://github.com/chaste/chaste-docker.git\n ```\n 3. Finally, if you want a bare container ready for you to clone and compile your own Chaste code, pull a `base` image with `docker pull chaste/base` (specifying an [available Ubuntu distribution](https://hub.docker.com/repository/docker/chaste/base/tags) if desired e.g. `chaste/base:focal`) Alternatively, build a fresh image by running the following command (omitting the `--build-arg GIT_TAG=` argument above, or explicitly passing `--build-arg GIT_TAG=-`, which will skip compiling Chaste within the image):\n ```\n docker build -t chaste:custom https://github.com/chaste/chaste-docker.git\n ```\n (When the container is running you may then edit `build_chaste.sh` in the `scripts` directory to configure the process with your own options before executing it.)\n\n2. Launch the container:\n ```\n docker run --init -it --rm -v chaste_data:/home/chaste chaste:custom\n ```\n The first time will take a little longer than usual as the volume has to be populated with data. For information on accessing the contents of this volume, see the section on [sharing data](#sharing-data-between-the-host-and-container).\n\n### Writing your own Dockerfile\n\n $\"Ten$ \n\nFor more advanced use cases, you can also include your own software, scripts and configuration by writing your own `Dockerfile`. To inherit the base configuration with the necessary dependencies and configuration for Chaste already set up, begin your `Dockerfile` with:\n```\nFROM chaste/base\n```\nor e.g. `chaste/base:focal` to specify a particular base image other than the `latest`. \n\nA full guide to writing a `Dockerfile` is beyond the scope of this project, however for more information, see the Docker [documentation](https://docs.docker.com/develop/develop-images/dockerfile_best-practices/) and [reference](https://docs.docker.com/engine/reference/builder/). There is also a handy list of Ten Simple Rules to help you get started! \n\n> :information_source: Pro tip! To write your own `Dockerfile`s, see [Nüst et al. 2020](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008316) for best practices. \n\nCitation\n--------\n\nIf you found this work helpful, please cite the following publication.\n\nCooper et al., (2020). Chaste: Cancer, Heart and Soft Tissue Environment. Journal of Open Source Software, 5(47), 1848. https://doi.org/10.21105/joss.01848\n\n[![DOI](https://joss.theoj.org/papers/10.21105/joss.01848/status.svg)](https://doi.org/10.21105/joss.01848)\n\n```\n@article{Chaste_2020,\n title = {Chaste: Cancer, Heart and Soft Tissue Environment},\n journal = {Journal of Open Source Software}\n publisher = {The Open Journal},\n year = {2020},\n month = {3},\n volume = {5},\n number = {47},\n pages = {1848},\n author = {Fergus R. Cooper and Ruth E. Baker and Miguel O. Bernabeu and Rafel Bordas and Louise Bowler and Alfonso Bueno-Orovio and Helen M. Byrne and Valentina Carapella and Louie Cardone-Noott and Jonathan Cooper and Sara Dutta and Benjamin D. Evans and Alexander G. Fletcher and James A. Grogan and Wenxian Guo and Daniel G. Harvey and Maurice Hendrix and David Kay and Jochen Kursawe and Philip K. Maini and Beth McMillan and Gary R. Mirams and James M. Osborne and Pras Pathmanathan and Joe M. Pitt-Francis and Martin Robinson and Blanca Rodriguez and Raymond J. Spiteri and David J. Gavaghan},\n doi = {10.21105/joss.01848},\n url = {https://doi.org/10.21105/joss.01848},\n}\n```\n\nAdditionally, if you found the \"Ten Simple Rules ...\" paper helpful for general advice or writing your own `Dockerfile`, please consider citing that too. \n\nNüst D, Sochat V, Marwick B, Eglen SJ, Head T, Hirst T, and Evans, BD. (2020) Ten simple rules for writing Dockerfiles for reproducible data science. PLoS Comput Biol 16(11): e1008316. https://doi.org/10.1371/journal.pcbi.1008316\n\n[![DOI](https://img.shields.io/badge/DOI-10.1371%2Fjournal.pcbi.1008316-yellow)](https://doi.org/10.1371/journal.pcbi.1008316)\n\n```\n@article{TSR_Dockerfiles_2020,\n title = {Ten Simple Rules for Writing Dockerfiles for Reproducible Data Science},\n journal = {PLOS Computational Biology},\n publisher = {Public Library of Science},\n year = {2020},\n month = {11},\n volume = {16},\n number = {11},\n pages = {1--24},\n author = {Daniel N{\\\"u}st and Vanessa Sochat and Ben Marwick and Stephen J. Eglen and Tim Head and Tony Hirst and Benjamin D. Evans},\n doi = {10.1371/journal.pcbi.1008316},\n url = {https://doi.org/10.1371/journal.pcbi.1008316},\n}\n```","has_starred","hub_user","immutable_tags_settings",{"_318":11,"_319":320},"enabled","rules",[321],".*","is_automated","permissions",{"_325":17,"_326":11,"_327":11},"read","write","admin","user","storage_size",491823097826,"isOrg","reponame","tag","sha256:7ca8505ed37753af0524c11285028153fd45100cf1ce8e339e7412d73ea7d4dc","canDeleteTags","isHubSbxKitsEnabled","currentTab","tagAttestations","displaySecurityMetadata","showSbxLogoOverride","routes/_layout.layers.$namespace.$reponame.$tag.(images).($imageUrlDigest)._index",{"_23":24,"_272":-7,"_270":-7,"_271":-7,"_25":343,"_31":334,"_347":-7,"_348":11},{"_27":28,"_29":30,"_31":32,"_33":34,"_35":36,"_37":344,"_63":64,"_65":30,"_66":67,"_68":69,"_70":71,"_72":73,"_74":46,"_75":64,"_76":56,"_77":17},[345,346],{"_40":41,"_31":42,"_43":44,"_45":46,"_47":48,"_49":50,"_51":44,"_52":-5,"_53":54,"_55":56,"_57":-5},{"_40":59,"_31":60,"_43":44,"_45":61,"_47":62,"_49":50,"_51":44,"_52":-5,"_53":34,"_55":56,"_57":-5},"imageWithLayers","hasPermissionToViewRepoSettings","actionData","errors"]

chaste/base:sha-566e31e