{"id":15546718,"url":"https://github.com/solida-core/solida","last_synced_at":"2025-04-23T18:09:43.488Z","repository":{"id":46815253,"uuid":"109510788","full_name":"solida-core/solida","owner":"solida-core","description":"SOLIDA is command-line solution that facilitate the reproducibility and portability of NGS pipelines. 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It can easily organize the deployment, the data management and the execution of a Snakemake based workflow.\n\n## Installation\n\nYou can install the latest stable version from PyPI\n```bash\npip install solida\n```\n\n## Requirements\n\nTo run Solida, Conda e Mamba must be presents in your computer.    \nTo install Conda, see [https://conda.io/miniconda.html](https://conda.io/miniconda.html) \nTo install Mamba, see [https://github.com/mamba-org/mamba](https://github.com/mamba-org/mamba)\n```bash\nconda install -c conda-forge mamba\n```\n\n\n## Usage\n\nTo check version:\n```bash\nsolida -v\n```\n\nTo list all the pipelines enabled, digit\n```bash\nsolida info\n```\n\nTo check if both pipeline and profile are available, digit:\n```bash\nsolida setup -l pipeline_label -p profile_label\n```\n\nBefore to deploy a pipeline, you have to create a project profile:\n```bash\nsolida setup -l pipeline_label -p profile_label --create-profile \n```\nSolida will create a yaml file named _profile_label.yaml_ into _~/solida_profiles_  \nEdit the _profile_label.yaml_ to match your environment settings.\n\nAfter that, deploy the pipeline into localhost with:\n```bash\nsolida setup -l pipeline_label -p profile_label --deploy \n```\nIf you want to deploy the pipeline into a remote host, add these \narguments:\n```bash\nsolida setup -l pipeline_label -p profile_label --deploy --host remote_host \n--remote-user username --connection ssh\n```\nwhere:  \n_--host_ is the hostname of the remote host  \n_--remote-user_ is a username available in the remote host  \n_--connection_ is the type of connection to use  \n\nPay attention, _remote_user_ have to be able to do ssh login into _remote_host_ \nwithout password (SSH Key-Based Authentication)\n\n### Script to execute the workflow\nSolida provides a bash script, _**run.project.sh**_, to facilitate the \nworkflow execution.  \n\n```\nrun.project.sh [-h] [-s Snakefile] -c FILENAME [-w DIR] [-p \"parameters\"] --script to execute a snakemake workflow\n\nwhere:\n    -h  show this help text\n    -s  path to a Snakefile different from the default one (Snakefile).\n    -c  path to the snakemake's configuration file.\n    -w  is the project's workdir label. Default is current timestamp.\n    -p  snakemake parameters as \"--rerun-incomplete --dryrun --keep-going --restart-time\"\n```\nUse _-s_ to specify a different Snakefile.  \n\nIf you don't give the script a workdir label (_-w_), a directory with the current \ntimestamp as label will be created and used to collect results into.\n\nOption _-c_ is mandatory and have to be the path to the snakemake's configuration file.\n \nOption _-p_ permit to provide the script all the snakemake parameters (don't \nforget to encapsulate them with \"\"\").\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsolida-core%2Fsolida","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsolida-core%2Fsolida","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsolida-core%2Fsolida/lists"}