Welcome to the git page of my MSc thesis project titled 'Microbes in captivity'. In this git you will find all the necessary files to recreate my thesis project, or
do a similar project of your own.
You will find all the necessary scripts to run the pipeline in the 'scripts_pipeline' folder. All the scripts I used to do my statistical analyses can be found
in the 'scripts_analysis' folder. Mind you, a lot of these scripts have hardcoded file paths in them, referring to e.g. the count_tables folder. Make sure to check
if these file paths suit your application.
## Getting started
In the 'metafiles' folder you will find all the files containing metadata that are used in the pipeline. Furthermore, it contains files with useful information
such as the links to the ftp sites from which I retrieved my genomes (based on Tantoso et al. (2022)), and the PRECISE 2.0 (Lamoureux et al. (in press)) metadata.
It is important to note that the scripts in the pipeline use metafiles. You will find examples of these metafiles in this folder as well. Please be careful when
creating these files yourself. The parsing is done based on length, so your metafile should be constructed as can be seen for each class of data (e.g. coculture or
monoculture) in this folder. Initially it should be constructed without the read direction included, once the read direction has been calculated, it should be
included in the metafile. Once again, it is vital to do this in this particular way, as the provided scripts use length based indexing, and as such, things will go
wrong if you do not do this. Consider yourself warned.
To make it easy for you to get started with GitLab, here's a list of recommended next steps.
The count_table folders contain the count tables produced in this research. These are useful should you wish to replicate the research I have done.
Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
Feel free to use and adjust the files in this git however you see fit, but don't forget to cite where necessary.
## Add your files
-[ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-[ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
Lamoureux, C. R., Decker, K. T., Sastry, A. V., McConn, J. L., Gao, Y., & Palsson, B. O. (in press). PRECISE 2.0 - an expanded high-quality RNA-seq compendium for
-[ ] [Set up project integrations](https://git.wur.nl/thimo.schotman/microbes-in-captivity/-/settings/integrations)
## Collaborate with your team
-[ ] [Invite team members and collaborators](https://docs.gitlab.com/ee/user/project/members/)
-[ ] [Create a new merge request](https://docs.gitlab.com/ee/user/project/merge_requests/creating_merge_requests.html)
-[ ] [Automatically close issues from merge requests](https://docs.gitlab.com/ee/user/project/issues/managing_issues.html#closing-issues-automatically)
-[ ] [Automatically merge when pipeline succeeds](https://docs.gitlab.com/ee/user/project/merge_requests/merge_when_pipeline_succeeds.html)
## Test and Deploy
Use the built-in continuous integration in GitLab.
-[ ] [Get started with GitLab CI/CD](https://docs.gitlab.com/ee/ci/quick_start/index.html)
-[ ] [Analyze your code for known vulnerabilities with Static Application Security Testing(SAST)](https://docs.gitlab.com/ee/user/application_security/sast/)
-[ ] [Deploy to Kubernetes, Amazon EC2, or Amazon ECS using Auto Deploy](https://docs.gitlab.com/ee/topics/autodevops/requirements.html)
-[ ] [Use pull-based deployments for improved Kubernetes management](https://docs.gitlab.com/ee/user/clusters/agent/)
-[ ] [Set up protected environments](https://docs.gitlab.com/ee/ci/environments/protected_environments.html)
***
# Editing this README
When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thank you to [makeareadme.com](https://www.makeareadme.com/) for this template.
## Suggestions for a good README
Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
## Name
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## Description
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## Usage
Use examples liberally, and show the expected output if you can. It's helpful to have inline the smallest example of usage that you can demonstrate, while providing links to more sophisticated examples if they are too long to reasonably include in the README.
## Support
Tell people where they can go to for help. It can be any combination of an issue tracker, a chat room, an email address, etc.
## Roadmap
If you have ideas for releases in the future, it is a good idea to list them in the README.
## Contributing
State if you are open to contributions and what your requirements are for accepting them.
For people who want to make changes to your project, it's helpful to have some documentation on how to get started. Perhaps there is a script that they should run or some environment variables that they need to set. Make these steps explicit. These instructions could also be useful to your future self.
You can also document commands to lint the code or run tests. These steps help to ensure high code quality and reduce the likelihood that the changes inadvertently break something. Having instructions for running tests is especially helpful if it requires external setup, such as starting a Selenium server for testing in a browser.
## Authors and acknowledgment
Show your appreciation to those who have contributed to the project.
## License
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## Project status
If you have run out of energy or time for your project, put a note at the top of the README saying that development has slowed down or stopped completely. Someone may choose to fork your project or volunteer to step in as a maintainer or owner, allowing your project to keep going. You can also make an explicit request for maintainers.
Tantoso, E., Eisenhaber, B., Kirsch, M., Shitov, V. A., Zhao, Z., & Eisenhaber, F. (2022). To kill or to be killed: pangenome analysis of Escherichia coli strains
reveals a tailocin specific for pandemic ST131. BMC Biology, 20(1). https://doi.org/10.1186/s12915-022-01347-7
