Command Line Interface

PathMe-Viewer commands.

pathme_viewer

PathMe

pathme_viewer [OPTIONS] COMMAND [ARGS]...

manage

Manage the database.

pathme_viewer manage [OPTIONS] COMMAND [ARGS]...

Options

-c, --connection <connection>

Cache connection. Defaults to sqlite:////home/docs/.bio2bel/bio2bel.db

drop

Delete all database entries

pathme_viewer manage drop [OPTIONS]

Options

-v, --debug

Turn on debugging.

-y, --yes
-c, --connection <connection>

Cache connection. Defaults to sqlite:////home/docs/.bio2bel/bio2bel.db

export-to-tsv

Export pathways to tsv

pathme_viewer manage export-to-tsv [OPTIONS]

Options

-c, --connection <connection>

Defaults to sqlite:////home/docs/.bio2bel/bio2bel.db

-a, --all

load

Load Pathways

pathme_viewer manage load [OPTIONS]

Options

-c, --connection <connection>

Cache connection. Defaults to sqlite:////home/docs/.bio2bel/bio2bel.db

-kp, --kegg_path <kegg_path>

KEGG data folder. Defaults to /home/docs/.pathme/kegg

-rp, --reactome_path <reactome_path>

Reactome data folder. Defaults to /home/docs/.pathme/reactome

-wp, --wikipathways_path <wikipathways_path>

WikiPathways data folder. Defaults to /home/docs/.pathme/wikipathways

-f, --flatten <flatten>

Flat complexes/composites. Defaults to False

-y, --yes

Skip confirmation

summarize

Summarizes Entries in Database

pathme_viewer manage summarize [OPTIONS]

Options

-c, --connection <connection>

Defaults to sqlite:////home/docs/.bio2bel/bio2bel.db

web

Run web service.

pathme_viewer web [OPTIONS]

Options

--host <host>

Flask host. Defaults to 0.0.0.0

--port <port>

Flask port. Defaults to 5000

--template <template>

Defaults to “../templates”

--static <static>

Defaults to “../static”

-v, --verbose