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 \
-password admin_password -url http://localhost:8080/apollo > my output.gff3
This command outputs the gff3 to standard output and can be redirected.
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.
add_users.groovy
Example:
add_users.groovy -username admin@webapollo.com -password admin_password \
-newuser newuser@test.com -newpassword newuserpass \
-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.
add_organism.groovy
Example:
add_organism.groovy -name yeast -url http://localhost:8080/apollo/ \
-directory /opt/apollo/yeast -username admin@webapollo.com -password admin_password
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.