AgustinPardo / pathwaytools-target-Integration

pathwaytools-target-Integration

Authors	Agustin Maria Pardo
Github	AgustinPardo
Email	[e-mail]

Requirements:

docker

pythoncyc

PathwayTools installer linux-64 24.0 (https://biocyc.org/download-bundle.shtml)

Install (image size: 3.77GB):

sudo docker build -t pathway:24.0 .

Run python server:

sudo docker run --name pathwaytools --volume $PWD:/localData --volume $PWD/PGDBs:/opt/data/ptools-local/pgdbs -d -p 5008:5008 pathway:24.0 

This comand links the . directory to localData container directory, and create the PGDB folder where the PGDBs reconstructions are stored. Also start a python server that listen on port 5008 to be queried using pythoncyc library (5008 default pythoncyc socket connection).

Create the PGDB:

sudo docker exec pathwaytools bash opt/pathway-tools/pathway-tools -no-patch-download -no-cel-overview -no-web-cel-overview -patho localData/ejemplo

This command create a PGBG itsef, and you should have the genetic-elements.dat, organism-params.dat, and annotation files inside a folder on the . directory. Check the ejemplo folder to see an example of those files or see PathoLogic Batch Mode section 7.6 of the PathwayTools user's manual for more information.

Restart the python service to see the new PGDB:

sudo docker container restart pathwaytools

once you successfully run the PGDB reconstrucion you should restart the python server to update the database served.

Test the new PGDB reconstruction:

import pythoncyc
PGDB_list=pythoncyc.all_orgids()
PGDB_list

meta = pythoncyc.select_organism("META")
all_pathways_list=meta.all_pathways(selector='all', base=True)
all_pathways_list

meta = pythoncyc.select_organism("TEST_2")
all_pathways_list=meta.all_pathways(selector='all', base=True)
all_pathways_list

Simple example of PGBDs python queries using pythoncyc library