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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.