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https://github.com/solida-core/solida
SOLIDA is command-line solution that facilitate the reproducibility and portability of NGS pipelines. It can easily organize the deployment, the data management and the execution of a Snakemake based workflow.
https://github.com/solida-core/solida
ansible ngs ngs-pipeline pipeline python reproducibility snakemake workflow yaml
Last synced: 2 months ago
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SOLIDA is command-line solution that facilitate the reproducibility and portability of NGS pipelines. It can easily organize the deployment, the data management and the execution of a Snakemake based workflow.
- Host: GitHub
- URL: https://github.com/solida-core/solida
- Owner: solida-core
- License: gpl-3.0
- Created: 2017-11-04T16:24:27.000Z (about 7 years ago)
- Default Branch: master
- Last Pushed: 2024-03-26T12:07:51.000Z (9 months ago)
- Last Synced: 2024-04-24T02:35:31.643Z (8 months ago)
- Topics: ansible, ngs, ngs-pipeline, pipeline, python, reproducibility, snakemake, workflow, yaml
- Language: Python
- Homepage:
- Size: 126 KB
- Stars: 4
- Watchers: 3
- Forks: 1
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- License: LICENSE
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README
# SOLIDA
[](https://travis-ci.org/solida-core/solida)
[](https://badge.fury.io/py/solida)
SOLIDA is command-line solution that facilitate the reproducibility and portability of NGS pipelines. It can easily organize the deployment, the data management and the execution of a Snakemake based workflow.
## Installation
You can install the latest stable version from PyPI
```bash
pip install solida
```
## Requirements
To run Solida, Conda e Mamba must be presents in your computer.
To install Conda, see [https://conda.io/miniconda.html](https://conda.io/miniconda.html)
To install Mamba, see [https://github.com/mamba-org/mamba](https://github.com/mamba-org/mamba)
```bash
conda install -c conda-forge mamba
```
## Usage
To check version:
```bash
solida -v
```
To list all the pipelines enabled, digit
```bash
solida info
```
To check if both pipeline and profile are available, digit:
```bash
solida setup -l pipeline_label -p profile_label
```
Before to deploy a pipeline, you have to create a project profile:
```bash
solida setup -l pipeline_label -p profile_label --create-profile
```
Solida will create a yaml file named _profile_label.yaml_ into _~/solida_profiles_
Edit the _profile_label.yaml_ to match your environment settings.
After that, deploy the pipeline into localhost with:
```bash
solida setup -l pipeline_label -p profile_label --deploy
```
If you want to deploy the pipeline into a remote host, add these
arguments:
```bash
solida setup -l pipeline_label -p profile_label --deploy --host remote_host
--remote-user username --connection ssh
```
where:
_--host_ is the hostname of the remote host
_--remote-user_ is a username available in the remote host
_--connection_ is the type of connection to use
Pay attention, _remote_user_ have to be able to do ssh login into _remote_host_
without password (SSH Key-Based Authentication)
### Script to execute the workflow
Solida provides a bash script, _**run.project.sh**_, to facilitate the
workflow execution.
```
run.project.sh [-h] [-s Snakefile] -c FILENAME [-w DIR] [-p "parameters"] --script to execute a snakemake workflow
where:
-h show this help text
-s path to a Snakefile different from the default one (Snakefile).
-c path to the snakemake's configuration file.
-w is the project's workdir label. Default is current timestamp.
-p snakemake parameters as "--rerun-incomplete --dryrun --keep-going --restart-time"
```
Use _-s_ to specify a different Snakefile.
If you don't give the script a workdir label (_-w_), a directory with the current
timestamp as label will be created and used to collect results into.
Option _-c_ is mandatory and have to be the path to the snakemake's configuration file.
Option _-p_ permit to provide the script all the snakemake parameters (don't
forget to encapsulate them with """).