A spiritual successor to Crawl
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README

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######################################################################################################
                                         Crawl, Number 2.
######################################################################################################


                                                                                           
More detailed documentation can be found in doc/index.html.

Crawl should run "out of the box", if you use the config files below, as these all point to public 
data or locally instantiated index clusters. Please note that all the example data used here are 
subject to the WSTI's data policies, see :

    http://www.sanger.ac.uk/legal/

The project is build with gradle, and includes a 
"gradlew" executable so you don't have to download and install gradle yourself. The first build will
take a while because it will download dependencies. OSX users please note that Java build tools like 
gradle need a properly set JAVA_HOME environmental variable. To build, do :

$ ./gradlew build

Also, as the build step involves downloading dependencies, and if you're behind a proxy, you may 
have to initially supply proxyHost and proxyPort Java settings, e.g. :

./gradlew build -Dhttp.proxyHost=wwwcache.sanger.ac.uk -Dhttp.proxyPort=3128


##############################################
# RUNNING OFF A CHADO DATABASE
##############################################

For a quick test run off the GeneDB public Chado database, try :

$ ./gradlew -Pconfig=resource-chado-public.properties jettyRunWar

and goto http://localhost:8080/services/index.html.

##############################################
# RUNNING OFF AN INDEXED GFF3 FILE
##############################################

If instead you want to try indexing a GFF file, try (assumes you're in bash) :

$ ./crawl gff2es -pe resource-elasticsearch-local.properties \
    -g  src/test/resources/data/Pf3D7_01.gff.gz \
    -o '{
    "ID":27, 
    "common_name":"Pfalciparum", 
    "genus":"Plasmodium", 
    "species":"falciparum", 
    "translation_table":11, 
    "taxonID":5833 
}' 
$ ./gradlew -Pconfig=resource-elasticsearch-local.properties jettyRunWar

and goto http://localhost:8080/services/index.html.