https://github.com/sing-group/compi-blast-example
A Compi pipeline based on the Nextflow blast-example: https://github.com/nextflow-io/blast-example
https://github.com/sing-group/compi-blast-example
Last synced: 6 months ago
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A Compi pipeline based on the Nextflow blast-example: https://github.com/nextflow-io/blast-example
- Host: GitHub
- URL: https://github.com/sing-group/compi-blast-example
- Owner: sing-group
- License: other
- Created: 2021-04-27T06:35:21.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2021-04-27T06:38:29.000Z (about 5 years ago)
- Last Synced: 2026-01-15T05:04:18.364Z (6 months ago)
- Language: Dockerfile
- Size: 2.93 KB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Compi pipeline blast example
This is a Compi example which ports to Compi a [Nextflow example pipeline](https://github.com/nextflow-io/blast-example) using BLAST.
## Prerequisites
- [Compi Development Kit (Compi-DK)](https://sing-group.org/compi/#downloads)
- [Docker](https://www.docker.com/)
## Building the pipeline
Move to the directory of the cloned respository of this pipeline and run `compi-dk build` inside it.
```bash
compi-dk build
```
## Running the pipeline with sample data
The Nextflow example contains some sample data:
- A fasta file, located at `/data/fasta.fa` inside the Docker image.
- A Blast database, located at `/blast-db/pdb/tiny` inside the Docker image.
In order to run the pipeline with the same sample data as Nextflow example, you have to run:
```bash
docker run -v /tmp:/result sing-group/compi-blast-example -o -- --chunkSize 2
```
A `results.txt` file will be created inside `/tmp` (see `-v /tmp:/result`).
## Running the pipeline with custom data
You can specify the `query` and `database` parameters of the pipeline. You will have to mount your data directory when running the Docker image. For example, `my-data-dir` could be a directory in your host machine containing both the fasta files and the BLAST database.
- `my-data-dir`
- `myfasta.fa`
- `/blast-db/mydatabase`
Next, you have to mount the data directory inside the Docker image when running it (see `-v my-data-dir:/data`) and pass the `query` and `database` parameters.
```bash
docker run -v /tmp:/result -v my-data-dir:/data sing-group/compi-blast-example -o -- --chunkSize 2 --query /data/myfasta.fa --database /data/blast-db/mydatabase
```