# Command line tools¶

The command line tools offer a number of interesting features that can be used to help setup and retrieve data from the application.

## Overview¶

The command line tools are located in docs/web_services/examples, and they are mostly small scripts that automate the usage of the the web services API.

### get_gff3.groovy¶

Example:

get_gff3.groovy -organism Amel_4.5 -username admin@webapollo.com \


This command can accept an -output argument to output to file, or the stdout can be redirected.

The -username and -password can be specified via the command line or if omitted, the user will be prompted.

### get_fasta.groovy¶

Example:

get_fasta.groovy -organism Amel_4.5 -username admin@webapollo.com \


This command can accept an -output argument to output to file, or the stdout can be redirected.

The -username and -password can be specified via the command line (similar to get_gff3.groovy) or if omitted, the user will be prompted.

Example:

add_users.groovy -username admin@webapollo.com -password admin_password \
-destinationurl http://localhost:8080/apollo


The -username and -password refer to the admin user, and they can also be specified via stdin instead of the command line if they are omitted.

A list of users specified in a csv file can also be used as input.

Example:

add_organism.groovy -name yeast -url http://localhost:8080/apollo/ \


The -directory refers to the jbrowse data directory containing the output from prepare-refseqs.pl, flatfile-to-json.pl, etc. The -blatdb is optional, -genus, and -species are optional.

The -username and -password refer to the admin user, and they can also be specified via stdin instead of the command line if they are omitted.

### delete_annotations_from_organism.groovy¶

Example:

docs/web_services/examples/groovy/delete_annotations_from_organism.groovy  -destinationurl http://localhost:8080/apollo\
-organismname honeybee2


This script will delete any annotations associated with a given organism.