https://github.com/berdal84/crispr-barista
Minimalist web UI for CRISPREsso2
https://github.com/berdal84/crispr-barista
bootstrap css flask html javascript
Last synced: 6 months ago
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Minimalist web UI for CRISPREsso2
- Host: GitHub
- URL: https://github.com/berdal84/crispr-barista
- Owner: berdal84
- Created: 2022-07-22T22:52:16.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2022-07-26T15:37:13.000Z (almost 4 years ago)
- Last Synced: 2023-02-27T18:02:29.029Z (over 3 years ago)
- Topics: bootstrap, css, flask, html, javascript
- Language: Python
- Homepage:
- Size: 602 KB
- Stars: 0
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# CRISPR Barista
*CRISPR Barista* is a simple UI to drive your command line CRISPResso2 program.
The program uses Python3.7+, Flask and Boostrap.
## Prerequisites
[CRISPResso2](https://github.com/pinellolab/CRISPResso2) must be installed using [bioconda method](https://github.com/pinellolab/CRISPResso2#bioconda) (running `CRISPResso2 -h` must not fail).
Python3.7+ must be installed in a Unix-like operating system (MacOS or Linux).
## Limitations
Handle only those parameters: `--fastq_r1`, `--fastq_r2`, `--amplicon_seq` and `--guide_seq`
In case you have a single `fastq` file containing 2 reads, you can check `split`, the program will split the files for you.
## Usage
### `./install.sh`
Initialize a local environment and install dependencies.
Python3 is required.
### `./run.sh`
Launches the application.
Once you see `* Running on http://127.0.0.1:5000 (Press CTRL+C to quit)` open `http://127.0.0.1:5000` with your favorite browser.
*Warning: do not deploy in production, use only localy*
### `./dev.sh`
Launches the application in debug mode.
## Captures
Main interface
Form filled using a double reads fastq file
CRISPResso2 results
