bioinformatics-tool-binary-path-resolution

bioinformatics-tool-binary-path-resolution

Summary

Resolve and verify the installation paths and executable availability of external bioinformatics tool binaries (e.g., bowtie2, samtools, iced) within a conda environment or system PATH, ensuring correct versions and runtime accessibility for a pipeline to function correctly.

When to use

When setting up a bioinformatics pipeline (such as HiC-Pro) that depends on multiple compiled or independently distributed binaries and you need to confirm that all required tools are installed, executable, meet version requirements (e.g., samtools ≥1.9), and can be located at runtime by the pipeline's configuration and execution steps.

When NOT to use

• The pipeline is already containerized (Docker/Singularity) and you are running it within that container — binary paths are pre-resolved by the container build.
• All required binaries are already manually installed in standard system locations (e.g., /usr/bin) and the pipeline successfully auto-detects them without configuration.
• You are using a pre-built conda lock file or manifest that guarantees binary availability — manual path resolution is not needed.

Inputs

• environment.yml or equivalent dependency specification file
• config-install.txt configuration file with tool path placeholders
• Pipeline source code directory

Outputs

• Activated conda environment with all dependencies installed
• Summary report documenting resolved tool paths, versions, and executability status
• config-system.txt or analogous generated configuration file with concrete tool paths

How to apply

Create a Conda environment from the pipeline's environment.yml specification file (e.g., using conda env create -f environment.yml -p /installation/path), then activate it and systematically verify each external tool: (1) check that the binary is in PATH and executable (e.g., which bowtie2); (2) confirm version constraints (e.g., samtools --version to verify ≥1.9); (3) for tools not included in the environment specification (such as iced, which is no longer part of HiC-Pro source), independently install from the upstream repository and verify importability in Python; (4) document all resolved paths, versions, and import status in a summary report. Use the pipeline's config-install.txt file to manually specify paths if automatic detection fails, and rely on the pipeline's built-in fallback mechanisms (which attempt automatic installation of bowtie2 and samtools if not detected in $PATH).