Improve portability of configurations

[jscgh]

To ease institutional deployments this PR refactors configuration to be standardised via the .env file.
Introduces required variable checks for job scripts, centralises and documents environment variable usage, and clarifies instructions.

• Added a comprehensive .env.example file listing all required and optional environment variables, with documentation for each, to serve as a template for site-specific configuration (template/.env)
• Introduced portal_default_* variables at the top of form.yml.erb and submit.yml.erb, and used ERB to set cluster, queue, and script defaults, making it easier to adapt the portal to new sites.
• Updated the README to clarify the distinction between portal-side defaults (in ERB templates) and runtime configuration (in .env), and provided improved instructions for site admins on how to configure and deploy the app.
• Refactored submit.yml.erb to decouple settings from hardcoded values.
• Minor bugfix for mkdir fasta missing -p.

Closes #50