Installation

A. Requirements

🔹 System Requirements

1. Operating System:

   • Linux (preferred)
   • macOS (works with Conda)
   • Windows (with WSL2)

2. Software Dependencies:

   • conda (Miniconda or Anaconda)
   • mamba (installed via Conda, if missing)
   • make (for running the Makefile)
   • bash (since Makefile runs Bash scripts)
   • git (recommended for version control)

B. 📖 How to Install & Run from Local Environment

1️⃣ Clone the Repository Clone the repository and go to the location where you installed the pipeline.

git clone git@github.com:PRIDE-Archive/file-download-stat.git
cd file-download-stat

2️⃣ Run the Installer Run the following command to set up the environment and install dependencies:

make setup      # Set up required variables
make install    # Run all checks and install dependencies

This will:

• Set up environment variables
• Install Conda if missing
• Install the required Conda environment (file_download_stat)
• Verify necessary paths

3️⃣ Copy Log Files Copy log files from the EBI server to your local machine.

 scp -r <username>@<server>:<path_to_log_files> <LOGS_DESTINATION_ROOT>

4️⃣ Run the Pipeline After the installation is complete, run the pipeline with:

scripts/run_stat_local.sh local 

C. 📖How to Install & Run from EBI Infrastructure

1️⃣ Fork the Repository
Fork the file-download-stat repository to your GitHub account.

2️⃣ Set Up EBI GitLab Repo
Set up a repository in GitLab to mirror the repository you forked from GitHub.

3️⃣ Customize params.config File
In the params folder, customize or add your <resource_name>-<environment>-params.config file to configure your pipeline parameters. For more details, visit parameters.

4️⃣ Set Up CI/CD Pipeline and Variables
Set up the CI/CD pipeline in GitLab. Be sure to configure any necessary environment variables that are required for your pipeline. For more details, visit GitLab CI/CD variables.

5️⃣ Deploy the Pipeline from GitLab
Deploy the pipeline from GitLab, making sure that the pipeline correctly uses your configuration.

6️⃣ Run make install Command
Go to the location where you installed the pipeline and run the following command to set up the environment and install dependencies:

make setup      # Set up required variables
make install    # Run all checks and install dependencies

7️⃣ Run the Pipeline After the installation is complete, run the pipeline with:

./run_download_stat.sh

8️⃣ Optionally, Set Up Seqera Environment If needed, you can optionally set up the Seqera environment to monitor the running pipelines. Please contact us for more information.