shell-environment-variable-resolution

shell-environment-variable-resolution

Summary

Automatically detect and resolve binary tool paths by querying the system $PATH environment variable when explicit paths are not provided in a configuration file. This skill enables pipeline setup to gracefully fall back to system-wide tool discovery, reducing manual configuration burden while maintaining the option for explicit path overrides.

When to use

Use this skill during pipeline installation or initialization when you need to locate required external binaries (e.g., bowtie2, samtools, R, Python) but the user has not explicitly provided their installation paths in a configuration file. Apply it when you want to support both automated and manual tool discovery, allowing users to either edit a config file with explicit paths or rely on standard system PATH lookups.

When NOT to use

• User has explicitly specified all tool paths in the configuration file and you are certain they are correct—direct use of the provided paths is more efficient than redundant PATH searching.
• The target environment does not use standard Unix $PATH conventions (e.g., embedded systems, containers with atypical path layouts) where 'which' will not work reliably.
• Pipeline execution has already begun and configuration is locked—re-resolving paths after initialization may corrupt running jobs or introduce inconsistency.

Inputs

• Configuration template file with placeholder entries (e.g., config-install.txt with PREFIX, BOWTIE2_PATH, SAMTOOLS_PATH, R_PATH, PYTHON_PATH, CLUSTER_SYS)
• System environment variables, particularly $PATH
• Shell environment context (access to 'which' command)

Outputs

• Environment-specific configuration file with resolved tool paths (e.g., config-system.txt)
• Read-only locked configuration file
• Binary discovery log or report (implicit)

How to apply

First, read the user-provided configuration file (e.g., config-install.txt) and identify which tool paths have been left unset or blank. For each unset path entry, use the shell 'which' command to search the system $PATH for the corresponding binary (e.g., 'which bowtie2', 'which samtools'). If a tool is not found in $PATH, flag it for automatic installation if supported (bowtie2 and samtools ≥1.9 can be auto-installed). After discovery or installation, validate that found/installed versions meet minimum requirements (e.g., samtools ≥1.9, Python >3.7). Compile all resolved paths—whether user-specified or auto-discovered—into a new, environment-specific configuration file (e.g., config-system.txt) with structured entries for each dependency. Finally, lock the generated configuration file as read-only to prevent accidental modification during pipeline execution.