Download Center
The download page provides the PathwayTools_V4 package, official libraries, and local-reuse guidance for reproducing the identification workflow.
Version: v1.0
Species: 789
Libraries: 6
Packages
3
Downloadable software packages
Official Libraries
6
Official library packages available for download
Species Slice
789
Species count represented by the public dataset
Genes
1381989
Enzyme-gene entries organized in the public dataset
PathwayTools_V4 Package
Software archive for local deployment and execution of PathwayTools_V4.
| Package | Description | Download |
|---|---|---|
| PathwayTools_V4 software package | PathwayTools_V4 package for local deployment and official-library reuse. | Download |
| PlantSME v1.0 SIF SHA256 checksum | SHA256 checksum file for PathwayTools_V1.sif. | Download |
| PlantSME v1.0 SIF container (PathwayTools_V1.sif) | PlantSME v1.0 container image; public filename PathwayTools_V1.sif; 20260604-patched build; SHA256 a5f13192c63a2ca295689584890b88935d26869862c7fc9f5a36a47570b21f64. | Download |
Official Libraries
Download the official PathwayTools_V4 libraries provided by this site for local identification or deployment migration.
| Library | Coverage | Version | Download |
|---|---|---|---|
|
Alkaloid Official Library
alkaloid/portable_core
|
Pathway：Alkaloid pathway
Module：Alkaloid portable pathway
|
v1.0 | Download |
|
Flavonoid Official Library
flavonoid/portable_core
|
Pathway：Flavonoid pathway
Module：Flavonoid portable pathway
|
v1.0 | Download |
|
Phenylpropanoid Official Library
phenylpropanoid/portable_core
|
Pathway：Phenylpropanoid pathway
|
v1.0 | Download |
|
Rosmarinic acid Official Library
rosmarinic_acid/portable_core
|
Pathway：Rosmarinic acid pathway
|
v1.0 | Download |
|
Steroid Official Library
steroid/portable_core
|
Pathway：Steroid pathway
Module：Steroid portable pathway
|
v1.0 | Download |
|
Terpenoid Official Library
terpenoid/portable_core
|
Pathway：Terpenoid pathway
Module：Terpenoid portable pathway
|
v1.0 | Download |
Deployment Guide
Official library packages are already built PathwayTools_V4 databases. After downloading, extract them and pass the extracted version directory to --db; do not run db build on these directories.
1Download and unpack the PathwayTools_V4 package
2Prepare the Python environment and install the dependencies listed in the package documentation
3Download the official library archives below and extract them into one local library root, for example ./plantsme_libraries
4Validate the extracted version directory with db validate, then use that directory as --db for identification
5If all six libraries are downloaded, use predict --db-root so the software can discover and run all portable libraries
For single-library runs, --db must point to the extracted version_* directory, for example ./plantsme_libraries/flavonoid/portable_core/version_20260517-portable.
mkdir -p plantsme_libraries tar -xzf plantsme_official_library_flavonoid-portable-20260517.tar.gz -C plantsme_libraries python PathwayTools.py check-env python PathwayTools.py db validate --db plantsme_libraries/flavonoid/portable_core/version_20260517-portable python PathwayTools.py run sample \ --db plantsme_libraries/flavonoid/portable_core/version_20260517-portable \ --input proteome.fa \ --species-id my_species \ --out results/my_species_flavonoid \ --config templates/config.example.yaml \ --mode full
Six-library example: extract all six official library archives into the same library root, inspect discovery with db info, then run predict.
for pkg in plantsme_official_library_*.tar.gz; do tar -xzf "$pkg" -C plantsme_libraries done python PathwayTools.py db info --root plantsme_libraries python PathwayTools.py predict proteome.fa \ --db-root plantsme_libraries \ --species-id my_species \ --out results/my_species_all_libraries \ --mode full
Species-Family Protein Downloads
To prevent bulk scraping of complete species or pathway outputs, this site only provides one-species by one-family candidate protein FASTA downloads; whole-pathway, whole-module, and all-results-per-species one-click downloads are not provided.
| Species | Family | Pathway | Members | Protein FASTA |
|---|---|---|---|---|
| No species-family protein FASTA files are currently available. | ||||