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A spiritual successor to Crawl
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andrewjpage/crawl2
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MMMMMMMMMMMMMMMMM8. 7MMMMMMMMMMMMMMMMMMO NMMMMMMMMMMMMMMM ,MMMMMMMMMMMMM: . . .... . 8MMMMMMMMMMMMO. ,MMMMMMMMMM. ~MMMMMMMMMM. ZMMMMMMMMMO MMMMMMMMMMMO. NMMMMMMN. $MMMMMMMMMMMM, MMMMMMMMMMMMM. DMMMMMMMMM? ?MMMMMM, .7MMMMMMMMMM~. .NMMMMMMMMMM.,NMMMMMMMN. ?MMMMMN?. . ,. ,. .,DMMMMMMMN. ,8MMMMMMMNN8$+~,,,,,:=IODNMMMMMMMMMM? +DMMMMMMMMMMMMMMMMMMMMMMMM$, ...:?7Z8DMNDO$7=. ###################################################################################################### 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 : https://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 https://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 https://localhost:8080/services/index.html.
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