Hi,
has anyone implemented the jbrowse_elasticsearch plugin in Apollo? I'm running from the docker container with an nginx reverse proxy and having trouble adding this plugin. How would I add this to the docker image, with the middleware as well? The reason we want to do this is the predicted gene model names we have in our tracks are not always intuitive so it's hard to find them by searching in Apollo (ie mTOR is ID'd as "serine/threonine-protein kinase mTOR", so if you just start typing mTOR you get no results). Wondering also if anyone else has encountered this problem and found good solutions, besides manipulating all of our tracks. Thanks so much, Michael This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. |
Aside from changing your gene identifiers, I think the full text search from elasticsearch could help. I forwarded some comments here about that https://github.com/elsiklab/jbrowse_elasticsearch/issues/7 Potentially data that is loaded in Apollo backend could use text similarity %like% or full text sql queries but for normal jbrowse tracks that are not loaded in the sql database, the jbrowse_elasticsearch plugin seems reasonable. -Colin On Tue, Nov 13, 2018 at 7:35 AM Michael Poeschla <[hidden email]> wrote: Hi, This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank. |
Michael, What problems are you running it when adding the plugins? Nathan
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Hi, I'm following the instructions from https://github.com/elsiklab/jbrowse_elasticsearch we have elasticsearch and the middleware app.js running. I was able to execute generate-names.pl and this seemed to work correctly from the terminal output. The changes also got picked up in the tracklist.json for the genome. But there is no sign of the elasticsearch plugin in web apollo...added the plugin to the config.groovy, and we have another jbrowse plugin (GC content) working fine so not sure what's the problem here. Thanks for all of your help! :) Michael From: "Nathan Dunn" <[hidden email]> To: "apollo" <[hidden email]> Sent: Tuesday, November 13, 2018 6:33:05 PM Subject: Re: [apollo] elastic search in genome apollo Michael, What problems are you running it when adding the plugins? Nathan
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Can you post your apollo config file?
Nathan
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Here it is - sorry for the late replies, I'm on europe time. environments { development { } test { } production { dataSource { dbCreate = "update" username = System.getenv("WEBAPOLLO_DB_USERNAME") ?: * password = System.getenv("WEBAPOLLO_DB_PASSWORD") ?: * driverClassName = "org.postgresql.Driver" dialect = "org.hibernate.dialect.PostgresPlusDialect" url = "jdbc:postgresql://${System.getenv("WEBAPOLLO_DB_HOST")?:"127.0.0.1"}/${System.getenv("WEBAPOLLO_DB_NAME")?:"apollo"}" properties { // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation jmxEnabled = false initialSize = 5 maxActive = 50 minIdle = 5 maxIdle = 25 maxWait = 10000 maxAge = 10 * 60000 timeBetweenEvictionRunsMillis = 5000 minEvictableIdleTimeMillis = 60000 validationQuery = "SELECT 1" validationQueryTimeout = 3 validationInterval = 15000 testOnBorrow = true testWhileIdle = true testOnReturn = false jdbcInterceptors = "ConnectionState" defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED } } dataSource_chado { dbCreate = "update" username = System.getenv("CHADO_DB_USERNAME") ?: * password = System.getenv("CHADO_DB_PASSWORD") ?: * driverClassName = "org.postgresql.Driver" dialect = "org.hibernate.dialect.PostgresPlusDialect" url = "jdbc:postgresql://${System.getenv("CHADO_DB_HOST")?:"127.0.0.1"}/${System.getenv("CHADO_DB_NAME")?:"chado"}" properties { // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation jmxEnabled = false initialSize = 5 maxActive = 50 minIdle = 5 maxIdle = 25 maxWait = 10000 maxAge = 10 * 60000 timeBetweenEvictionRunsMillis = 5000 minEvictableIdleTimeMillis = 60000 validationQuery = "SELECT 1" validationQueryTimeout = 3 validationInterval = 15000 testOnBorrow = true testWhileIdle = true testOnReturn = false jdbcInterceptors = "ConnectionState" defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED } } } } apollo { default_minimum_intron_size = System.getenv("WEBAPOLLO_MINIMUM_INTRON_SIZE") ? System.getenv("WEBAPOLLO_MINIMUM_INTRON_SIZE").toInteger() : 1 history_size = System.getenv("WEBAPOLLO_HISTORY_SIZE") ? System.getenv("WEBAPOLLO_HISTORY_SIZE").toInteger() : 0 overlapper_class = System.getenv("WEBAPOLLO_OVERLAPPER_CLASS") ?: "org.bbop.apollo.sequence.OrfOverlapper" use_cds_for_new_transcripts = System.getenv("WEBAPOLLO_CDS_FOR_NEW_TRANSCRIPTS").equals("true") // will default to false feature_has_dbxrefs = System.getenv("WEBAPOLLO_FEATURE_HAS_DBXREFS") ?: true feature_has_attributes = System.getenv("WEBAPOLLO_FEATURE_HAS_ATTRS") ?: true feature_has_pubmed_ids = System.getenv("WEBAPOLLO_FEATURE_HAS_PUBMED") ?: true feature_has_go_ids = System.getenv("WEBAPOLLO_FEATURE_HAS_GO") ?: true feature_has_comments = System.getenv("WEBAPOLLO_FEATURE_HAS_COMMENTS") ?: true feature_has_status = System.getenv("WEBAPOLLO_FEATURE_HAS_STATUS") ?: true translation_table = "/config/translation_tables/ncbi_" + (System.getenv("WEBAPOLLO_TRANSLATION_TABLE") ?: "1") + "_translation_table.txt" get_translation_code = System.getenv("WEBAPOLLO_TRANSLATION_TABLE") ? System.getenv("WEBAPOLLO_TRANSLATION_TABLE").toInteger() : 1 // ADDED BLAT AND SET PATH TO BIN sequence_search_tools = [ blat_nuc: [ search_exe: "/usr/local/bin/blat", search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineNucleotideToNucleotide", name: "Blat nucleotide", params: "" ], blat_prot: [ search_exe: "/usr/local/bin/blat", search_class: "org.bbop.apollo.sequence.search.blat.BlatCommandLineProteinToNucleotide", name: "Blat protein", params: "" ] ] // TODO: should come from config or via preferences database splice_donor_sites = System.getenv("WEBAPOLLO_SPLICE_DONOR_SITES") ? System.getenv("WEBAPOLLO_SPLICE_DONOR_SITES").split(",") : ["GT"] splice_acceptor_sites = System.getenv("WEBAPOLLO_SPLICE_ACCEPTOR_SITES") ? System.getenv("WEBAPOLLO_SPLICE_ACCEPTOR_SITES").split(",") : ["AG"] gff3.source = System.getenv("WEBAPOLLO_GFF3_SOURCE") ?: "." google_analytics = System.getenv("WEBAPOLLO_GOOGLE_ANALYTICS_ID") ?: ["UA-62921593-1"] admin{ username = System.getenv("APOLLO_ADMIN_EMAIL") ?: * password = System.getenv("APOLLO_ADMIN_PASSWORD") ?: * firstName = System.getenv("APOLLO_ADMIN_FIRST_NAME") ?: * lastName = System.getenv("APOLLO_ADMIN_LAST_NAME") ?: * } } jbrowse { git { url = "https://github.com/GMOD/jbrowse" tag = "maint/1.12.5-apollo" } plugins { WebApollo{ included = true } NeatHTMLFeatures{ included = System.getenv("WEBAPOLLO_JBROWSE_PLUGIN_NEATHTML") ?: true } NeatCanvasFeatures{ included = System.getenv("WEBAPOLLO_JBROWSE_PLUGIN_NEATCANVAS") ?: true } RegexSequenceSearch{ included = true } HideTrackLabels{ included = true } //EDIT: ADDED GC CONTENT GCContent{ git = 'https://github.com/cmdcolin/GCContent' branch = 'master' alwaysRecheck = "true" alwaysPull = "true" } //EDIT: ADDS ELASTIC SEARCH PLUGIN ElasticSearch{ git = 'https://github.com/elsiklab/jbrowse_elasticsearch' branch = 'master' alwaysRecheck = "true" alwaysPull = "true" } } } From: "Lbl" <[hidden email]> To: "apollo" <[hidden email]> Sent: Thursday, November 15, 2018 12:30:50 AM Subject: Re: [apollo] elastic search in genome apollo Can you post your apollo config file? Nathan
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Thanks. Also on Europe time for another 20 minutes.
Can you also post any other specifics of failure? Have you installed elasticsearch via docker or manually ? Nathan
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hi, elasticsearch was installed with docker. Here's the tracklist.json for the organism that we generated the index for. Is there any other info I could provide that would help? { "elasticIndexName" : "nfz", "elasticSearchUrl" : "localhost:3000", "formatVersion" : 1, "names" : { "type" : "Hash", "url" : "names/" }, "plugins" : [ "ElasticSearch" ], "tracks" : [ { "category" : "Reference sequence", "chunkSize" : 20000, "key" : "Reference sequence", "label" : "DNA", "seqType" : "dna", "storeClass" : "JBrowse/Store/Sequence/StaticChunked", "type" : "SequenceTrack", "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-" }, { "bicolor_pivot" : 0.5, "label" : "GC Content", "storeClass" : "JBrowse/Store/SeqFeature/SequenceChunks", "type" : "GCContent/View/Track/GCContentXY", "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-" }, { "compress" : 0, "key" : "Repeats", "label" : "Repeats", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "style" : { "className" : "feature" }, "trackType" : "JBrowse/View/Track/CanvasFeatures", "type" : "JBrowse/View/Track/CanvasFeatures", "urlTemplate" : "tracks/Repeats/{refseq}/trackData.json" }, { "compress" : 0, "key" : "Annotation", "label" : "Annotationfromsumgff", "storeClass" : "JBrowse/Store/SeqFeature/NCList", "style" : { "className" : "feature" }, "trackType" : "CanvasFeatures", "type" : "CanvasFeatures", "urlTemplate" : "tracks/Annotationfromsumgff/{refseq}/trackData.json" } ] } From: "Lbl" <[hidden email]> To: "apollo" <[hidden email]> Sent: Thursday, November 15, 2018 11:33:03 AM Subject: Re: [apollo] elastic search in genome apollo Thanks. Also on Europe time for another 20 minutes. Can you also post any other specifics of failure? Have you installed elasticsearch via docker or manually ? Nathan
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So you are saying that the plugin is not being added e.g. you don't have a menu item for the ElasticSearch dialog in jbrowse? -Colin On Thu, Nov 15, 2018 at 9:07 AM Michael Poeschla <[hidden email]> wrote:
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yes - we don't see anything in the browser Thanks, Michael From: "Colin" <[hidden email]> To: "apollo" <[hidden email]> Sent: Thursday, November 15, 2018 7:09:45 PM Subject: Re: [apollo] elastic search in genome apollo So you are saying that the plugin is not being added e.g. you don't have a menu item for the ElasticSearch dialog in jbrowse? -Colin On Thu, Nov 15, 2018 at 9:07 AM Michael Poeschla <[hidden email]> wrote:
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Sorry for the late response.
Can you provide the browser console logs and any tomcat logs (catalina.out)? Your modified docket file may be helpful as well. Nathan
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Hi, here are the logs, docker-compose, actual dockerfile and start and testing of npm (below). I've also added the tomcat logs as an attachment. docker-compose: -- version: "3.2" services: apollo: volumes: - ./data/extdata/:/data - postgres-data:/var/lib/postgresql - ./config/tomcat/server.xml:/var/lib/tomcat8/conf/server.xml:ro - ./config/tomcat/setenv.sh:/usr/share/tomcat8/bin/setenv.sh environment: APOLLO_ADMIN_[hidden email] restart: always links: - elasticsearch:elasticsearch nginx: image: library/nginx:alpine restart: always volumes: - ./config/nginx/nginx.conf:/etc/nginx/nginx.conf:ro - ./config/secrets:/secrets:ro ports: - 80:80 - 443:443 links: - apollo:apollo elasticsearch: image: elasticsearch:6.4.2 container_name: elasticsearch environment: - cluster.name=docker-cluster - bootstrap.memory_lock=true - "ES_JAVA_OPTS=-Xms512m -Xmx512m" ulimits: memlock: soft: -1 hard: -1 volumes: - esdata1:/usr/share/elasticsearch/data volumes: postgres-data: esdata1: driver: local -- The actual Dockerfile: -- # WebApollo # VERSION 2.1.X FROM tomcat:8-jre8 MAINTAINER Eric Rasche <[hidden email]>, Anthony Bretaudeau <[hidden email]>, Nathan Dunn <[hidden email]> ENV DEBIAN_FRONTEND noninteractive RUN apt-get -qq update --fix-missing && \ apt-get --no-install-recommends -y install \ git build-essential maven tomcat8 libpq-dev postgresql-common openjdk-8-jdk wget \ postgresql postgresql-client xmlstarlet netcat libpng-dev \ zlib1g-dev libexpat1-dev ant curl ssl-cert zip unzip RUN curl -sL https://deb.nodesource.com/setup_8.x | bash - RUN apt-get -qq update --fix-missing && \ apt-get --no-install-recommends -y install nodejs && \ apt-get autoremove -y && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* RUN cp /usr/lib/jvm/java-8-openjdk-amd64/lib/tools.jar /usr/lib/jvm/java-8-openjdk-amd64/jre/lib/ext/tools.jar && \ useradd -ms /bin/bash -d /apollo apollo ENV WEBAPOLLO_VERSION 99c7e54c6e74fbc6705d57de216c9b14b2bfb03b RUN curl -L <a href="https://github.com/GMOD/Apollo/archive/${WEBAPOLLO_VERSION}.tar.gz" class="" target="_blank" data-mce-href="https://github.com/GMOD/Apollo/archive/${WEBAPOLLO_VERSION}.tar.gz">https://github.com/GMOD/Apollo/archive/${WEBAPOLLO_VERSION}.tar.gz | tar xzf - --strip-components=1 -C /apollo # install grails COPY build.sh /bin/build.sh ADD apollo-config.groovy /apollo/apollo-config.groovy RUN chown -R apollo:apollo /apollo RUN curl -s "http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/blat" -o /usr/local/bin/blat RUN chmod +x /usr/local/bin/blat USER apollo RUN curl -s get.sdkman.io | bash RUN /bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install grails 2.5.5" RUN /bin/bash -c "source $HOME/.sdkman/bin/sdkman-init.sh && yes | sdk install gradle 3.2.1" RUN /bin/bash -c "source $HOME/.profile && source $HOME/.sdkman/bin/sdkman-init.sh && /bin/bash /bin/build.sh" USER root ENV CATALINA_HOME=/var/lib/tomcat8 RUN rm -rf ${CATALINA_HOME}/webapps/* && \ cp /apollo/apollo*.war ${CATALINA_HOME}/apollo.war ENV CONTEXT_PATH ROOT # Download chado schema RUN wget --quiet https://github.com/erasche/chado-schema-builder/releases/download/1.31-jenkins97/chado-1.31.sql.gz -O /chado.sql.gz && \ gunzip /chado.sql.gz RUN wget https://optinsoft.net/pic/ipgen2.png -O test.png ADD launch.sh /launch.sh CMD "/launch.sh" -- Starting npm inside the container: root@995955a711e1:/var/lib/tomcat8/webapps/ROOT/jbrowse/plugins/ElasticSearch# npm start > jbrowse_elasticsearch@1.0.4 start /var/lib/tomcat8/webapps/ROOT/jbrowse/plugins/ElasticSearch > node ./bin/www testing access with curl: root@995955a711e1:/usr/local/tomcat# curl http://localhost:3000 {"hits":[],"total":0}root@995955a711e1:/usr/local/tomcat# content of ElasticSearchPlugin: ^Croot@995955a711e1:/var/lib/tomcat8/webapps/ROOT/jbrowse/plugins/ElasticSearch# ls -la total 68 drwxr-x--- 10 tomcat8 tomcat8 271 Nov 14 17:10 . drwxr-x--- 12 tomcat8 tomcat8 223 Nov 14 16:34 .. -rw-r----- 1 tomcat8 tomcat8 594 Nov 14 16:16 .eslintrc -rw-r----- 1 tomcat8 tomcat8 290 Nov 14 16:16 .travis.yml -rw-r----- 1 tomcat8 tomcat8 686 Nov 14 16:16 ChangeLog.md -rw-r----- 1 tomcat8 tomcat8 810 Nov 14 16:16 Makefile.PL -rw-r----- 1 tomcat8 tomcat8 5157 Nov 14 16:16 README.md -rw-r----- 1 tomcat8 tomcat8 1888 Nov 14 16:44 app.js drwxr-x--- 2 tomcat8 tomcat8 66 Nov 14 16:34 bin drwxr-x--- 2 tomcat8 tomcat8 22 Nov 14 16:34 css drwxr-x--- 2 tomcat8 tomcat8 22 Nov 14 16:34 docs drwxr-x--- 2 tomcat8 tomcat8 45 Nov 14 16:34 img drwxr-x--- 3 tomcat8 tomcat8 65 Nov 14 16:34 js drwxr-xr-x 24 root root 4096 Nov 14 17:10 node_modules -rw-r----- 1 tomcat8 tomcat8 25820 Nov 14 17:10 package-lock.json -rw-r----- 1 tomcat8 tomcat8 725 Nov 14 16:16 package.json -rw-r----- 1 tomcat8 tomcat8 727 Nov 14 16:16 setup.sh drwxr-x--- 3 tomcat8 tomcat8 19 Nov 14 16:34 src drwxr-x--- 3 tomcat8 tomcat8 33 Nov 14 16:34 test ..And the logs are attached. Thanks! Michael From: "Lbl" <[hidden email]> To: "apollo" <[hidden email]> Sent: Saturday, November 17, 2018 4:06:58 AM Subject: Re: [apollo] elastic search in genome apollo Sorry for the late response. Can you provide the browser console logs and any tomcat logs (catalina.out)? Your modified docket file may be helpful as well. Nathan
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Thanks. Will have a look.
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I went and tested this and I tried testing adding the plugin to apollo-config.groovy and was getting an error about plugins/ElasticSearch/js/main.js not being loaded apollo run-local. I can see that it gets downloaded to jbrowse-download/plugins/ElasticSearch but it was giving me that error there still. I also ran apollo deploy and then unzipped and the jbrowse plugins folder did not contain ElasticSearch plugin Screenshot attached and apollo-config.groovy snippet here jbrowse { Â Â plugins { Â Â Â Â ElasticSearch { Â Â Â Â Â Â git = 'https://github.com/elsiklab/jbrowse_elasticsearch' Â Â Â Â Â Â branch = 'master' Â Â Â Â Â Â alwaysRecheck = "true" Â Â Â Â Â Â alwaysPull = "true" Â Â Â Â } Â Â } } -Colin On Tue, Nov 20, 2018 at 6:57 PM Nathan Dunn <[hidden email]> wrote:
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Thanks for testing Colin. I wasn’t sure the exact plugin to test with. I did get it to deploy off of master. I did an ./apollo clean-all I did an ./apollo deploy first (not sure if that made any difference, but it should not have). My config is the sample-h2-config.groovy file with the snippet that Colin provided below. That being said, I didn’t do a full test with the elastic search plugin, but this seems to install it correctly and I get an organism window, etc. when I load the volvox data. Nathan // default username/password on h2 are given here. see docs for adjusting dataSource { pooled = true jmxExport = true driverClassName = "org.h2.Driver" username = "sa" password = "" } // environment specific settings environments { development { // sample config to turn on debug logging in development e.g. for apollo run-local log4j.main = { debug "grails.app" } // sample config to edit apollo specific configs in development mode apollo { gff3.source = "testing" } dataSource { // NOTE: this is in memory, so it will be deleted. dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', '' url = "jdbc:h2:AnnotationDatabase:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE" } } test { dataSource { dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', '' url = "jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE" } } //note: not necessarily recommended to use h2 in production mode. see precautions production { dataSource { dbCreate = "update" //NOTE: production mode uses file instead of mem database //NOTE: Please specify the appropriate file path, otherwise /tmp/prodDb will be used. url = "jdbc:h2:/opt/apollo/h2/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE" properties { // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation jmxEnabled = true initialSize = 5 maxActive = 50 minIdle = 5 maxIdle = 25 maxWait = 10000 maxAge = 10 * 60000 timeBetweenEvictionRunsMillis = 5000 minEvictableIdleTimeMillis = 60000 validationQuery = "SELECT 1" validationQueryTimeout = 3 validationInterval = 15000 testOnBorrow = true testWhileIdle = true testOnReturn = false jdbcInterceptors = "ConnectionState" defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED } } } } // Uncomment to change the default memory configurations //grails.project.fork = [ // test : false, // // configure settings for the run-app JVM // run : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false], // // configure settings for the run-war JVM // war : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false], // // configure settings for the Console UI JVM // console: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024] //] // Uncomment to make changes // jbrowse { git { tag = "maint/1.12.5-apollo" alwaysPull = true alwaysRecheck = true } plugins { NeatHTMLFeatures{ included = true } NeatCanvasFeatures{ included = true } RegexSequenceSearch{ included = true } HideTrackLabels{ included = true } ElasticSearch { branch = 'master' alwaysRecheck = "true" alwaysPull = "true" } // MyVariantInfo { // git = 'https://github.com/GMOD/myvariantviewer' // branch = 'master' // alwaysRecheck = "true" // alwaysPull = "true" // } // SashimiPlot { // git = 'https://github.com/cmdcolin/sashimiplot' // branch = 'master' // alwaysPull = "true" // } } }
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the reason the plugin didn't show up turned out to be because i was editing both the apollo-config.groovy and the tracklist.json as you would for jbrowse. When I removed that line from the tracklist.json, the elasticsearch popped up immediately. This was a while back, just remembered to add it here in case anyone else runs into this kind of issue. Best, Michael From: "Nathan Dunn" <[hidden email]> To: "apollo" <[hidden email]> Sent: Wednesday, November 21, 2018 9:05:13 PM Subject: Re: [apollo] elastic search in genome apollo Thanks for testing Colin. I wasn’t sure the exact plugin to test with. I did get it to deploy off of master. I did an ./apollo clean-all I did an ./apollo deploy first (not sure if that made any difference, but it should not have). My config is the sample-h2-config.groovy file with the snippet that Colin provided below. That being said, I didn’t do a full test with the elastic search plugin, but this seems to install it correctly and I get an organism window, etc. when I load the volvox data. Nathan // default username/password on h2 are given here. see docs for adjusting dataSource { pooled = true jmxExport = true driverClassName = "org.h2.Driver" username = "sa" password = "" } // environment specific settings environments { development { // sample config to turn on debug logging in development e.g. for apollo run-local log4j.main = { debug "grails.app" } // sample config to edit apollo specific configs in development mode apollo { gff3.source = "testing" } dataSource { // NOTE: this is in memory, so it will be deleted. dbCreate = "update" // one of 'create', 'create-drop', 'update', 'validate', '' url = "jdbc:h2:AnnotationDatabase:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE" } } test { dataSource { dbCreate = "create-drop" // one of 'create', 'create-drop', 'update', 'validate', '' url = "jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE" } } //note: not necessarily recommended to use h2 in production mode. see precautions production { dataSource { dbCreate = "update" //NOTE: production mode uses file instead of mem database //NOTE: Please specify the appropriate file path, otherwise /tmp/prodDb will be used. url = "jdbc:h2:/opt/apollo/h2/prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE" properties { // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation jmxEnabled = true initialSize = 5 maxActive = 50 minIdle = 5 maxIdle = 25 maxWait = 10000 maxAge = 10 * 60000 timeBetweenEvictionRunsMillis = 5000 minEvictableIdleTimeMillis = 60000 validationQuery = "SELECT 1" validationQueryTimeout = 3 validationInterval = 15000 testOnBorrow = true testWhileIdle = true testOnReturn = false jdbcInterceptors = "ConnectionState" defaultTransactionIsolation = java.sql.Connection.TRANSACTION_READ_COMMITTED } } } } // Uncomment to change the default memory configurations //grails.project.fork = [ // test : false, // // configure settings for the run-app JVM // run : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false], // // configure settings for the run-war JVM // war : [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024, forkReserve: false], // // configure settings for the Console UI JVM // console: [maxMemory: 2048, minMemory: 64, debug: false, maxPerm: 1024] //] // Uncomment to make changes // jbrowse { git { tag = "maint/1.12.5-apollo" alwaysPull = true alwaysRecheck = true } plugins { NeatHTMLFeatures{ included = true } NeatCanvasFeatures{ included = true } RegexSequenceSearch{ included = true } HideTrackLabels{ included = true } ElasticSearch { branch = 'master' alwaysRecheck = "true" alwaysPull = "true" } // MyVariantInfo { // git = 'https://github.com/GMOD/myvariantviewer' // branch = 'master' // alwaysRecheck = "true" // alwaysPull = "true" // } // SashimiPlot { // git = 'https://github.com/cmdcolin/sashimiplot' // branch = 'master' // alwaysPull = "true" // } } }
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Thanks for reporting the workaround for this. In the future I’ll try to make sure that this doesn’t kill it so you can hopefully re-use that directory as a Browse directory. Cheers, Nathan
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