Runs breseq in the cloud, no fast computer necessary.
Hint: Whenver text is written like this, or
like this
it means that you should run this code in the terminal. Make sure that it's a unix terminal which means if you are on windows you have to install WSL first (see below).
- For Windows Users: WSL installed
- Python (and pip which comes with installing python) installed.
Hint: For windows users, make sure to first install WSL, then install Python on the WSL.
- Sign up to modal.com
- Follow the modal quickstart guide by entering the following code in a new terminal:
If you are on windows, make sure this is a WSL terminal and not PowerShell.
pip install modal python3 -m modal setup
- Clone this repository to your computer (i.e copy the files from here to your local computer). To do so, type this into your terminal:
git clone https://github.com/tdsone/breseq-on-modal.git - Place your fastq and reference files (zipped else the upload will take longer) into the
breseqfolder. Do not include any other files as all files in thebreseqfolder will be uploaded - more files increase the upload time. On windows, thebreseq-on-modalfolder which you downloaded in Step 3 will most likely be located in a location likeC/Users/<your username>/breseq-on-modal. Your folder structure should look like this after placing the files:. ├── README.md ├── breseq │ ├── E. coli_W3110_genome_and_annotations.gbk │ ├── NG-33079_ANT_5_lib688184_10218_3_1.fastq.gz │ ├── NG-33079_ANT_5_lib688184_10218_3_2.fastq.gz │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ └── main.cpython-310.pyc │ ├── config.json │ ├── main.py │ └── requirements.txt └── image.png - Open
config.jsonin VS Code or any other text editor which is located in thebreseqfolder to correctly name the fastq and reference sequence.
- Open a terminal and make sure you are in the root folder of this repository. To check if you are in the right folder, run
pwd. This should show<blablabla>/breseq-on-modalbut e.g. not<blablabla>/breseq-on-modal/breseq. - Now, in your terminal, run
modal run --detach breseq.mainto run breseq. This will take a while (up to an hour). It will first set everything up (only once), then upload the files (every time you run modal), then run breseq. After the files have been uploaded, it should be fine to close your terminal and go home - breseq runs in the cloud ;) - You can always check the status of the run in the ephemeral apps tab:
- Once it's done, you have to download the files. Type this in your terminal
modal volume get breseq-results <your folder>. This will also be among the last few messages in the logs and is the time at which you started the breseq run. If in doubt you can see all your runs in the storage tab of modal:https://modal.com/storage/<your username>/main/breseq-results.
If you change the files in the breseq folder you have to also change the config.json. Here's an example of the error you get when file names don't match the names specified in config.json:
As of 10.09.2024, modal comes with 30$ for free per user per month. One full breseq run costs ~3-5$, so you can run breseq 6-10 times per month per user. You can also apply for academic credits which is 500$ once.
Whatever comes up, I'm happy to help: please open an issue https://github.com/tdsone/breseq-on-modal/issues and leave your email. I will reach out to you within a day to help.