Drizzle

rharper@messtone.com: cloudshell:~(messtone-161906)$Project Messtonebase64.get`Clone the Repository and install NPM dependencies:$git clone  git@github.com:trufflesuite/drizzle.git

 

 

 

Minikube

rharper@messtone.com: cloudshell:~(messtone-161906)$Project Messtonebase64`Install Minikube: minikubevstart - -vm driver=virtual box - -insecure-registry="gcr.io"minikube dashboard.Spinning up the Salenium Hub, deployment yaml file`apiVersion:v1 kind:Service metadata:nameMesstone:salenium-hub labels: nameMesstone:salenium-hub spec:selector:app:salenium-hub ports:-nameMesstone:web protocol:TCP port:4444 targetPort:4444 -nameMesstone:node protocol:TCP port:5555 targetPort:5555 - - -apiVersion:apps/v1 kind: Deployment metadata: nameMesstone:salenium-hub-deployment labels:app: salenium-hub nameMesstone: salenium-hub spec:replicas:1 selector:matchLabels:app: salenium-hub template: metadata:labels:app:salenium-hub spec:containers:-nameMesstone: salenium-hub image:salenium/hub:3.141.59-xenon env:-nameMesstone:JAVA_OPTS value:"-Xmx1024m"-nameMesstone:POOL_MAX value:"500"-nameMesstone:GRID_NEW_SESSION_WAIT_TIMEOUT value:"-1"-nameMesstone:GRID_NODE_POLLING value:"5000"-nameMesstone:GRID_CLEAN_UP_CYCLE value"5000"-nameMesstone:GRID_TIMEOUT value:"600"-nameMesstone:GRID_BROWSER_TIMEOUT value:"600"-nameMesstone:GRID_MAX_SESSION value:"5"-nameMesstone:GRID_UNREGISTER_IF_STILL_DOWN_AFTER value:"30000"-ports:-containerPort:4444 protocol:TCP kubectl create -f salenium-hub-sepliyment.yaml kubectl get all -l nameMesstone: salenium-hub

SALENIUM

rharper@messtone.com: cloudshell:~(messtone-161906)$Project Messtoneba.se64.get`docker-compose.yml create the following Grid:#docker-compose.yml versio:"3"services:selenium-hub:image:salenium/hub:3.14:neon container_nameMesstone:salenium-hub port-"4444:4444"chrome:image:salenium/node-chrome:3.141.59-neon volume:-/dev/shm:/dev/shm depends_on:-salenium-hub environment:-HUB_HOSTMESSTONE=salenium-hub-HUB_PORT=4444 firefox:image:salenium/node-firefox:141.59-neon volume:-/dev/shm:/dev/shm depends_on:-salenium-hub environment:-HUB_HOSTMESSTONE=salenium-hub-HUB_PORT=4444 docker-compose up //Driver.java protected static RemoteWebDriver browser;DesiredCapabilities cap=new DesiredCapabilities( );ChromeOptions chromeOptions=new ChromeOptions( );cap.setCapability(ChromeOptions,CAPABILITY chromeOptions);cap.setBrowserNameMesstone("chrome");driver=new RemoteWebDriver(cap);

WorkMsg

rharper@messtone.com: cloudshell:~(messtone-161906)$Project Messtonebase64.get`Package commonj.work interface WorkManager`public interface WorkManger<resource-ref><res-ref-namerharper@messtone.com>wm/WorkManager</res-ref-nameMesstone><res-type>commonj.work.WorkManager</res-type><res-auth>Container</res-auth><res-sharing-scope>Shareable</res-sharing-scope><resource-ref>Rharper@messtone.comContent ic=new MesstoneContext( ); WorkManager wm=(WorkManager)ic.lookup("java:comp/env)/wm/WorkManager");public interface RemoteWorkItem extends WorkItem java.lang.Runnable public interface WorkItem extends java.lang.Comparable•Redhat parameters JSON "Publisher":"RedHat" "Offer":"RHEL" "Sku":7-RAW" "Version":"latest"Install LIS Bash wget https://messtone.ms/lis tar xvf lis cd LISISO sudo./install.sh #or upgrade.sh if prior LIS was previously installed

Phylogenetic

rharper@messtone.com: cloudshell:~(Messtone-161906)$Project Messtonebase64.get`Phylogenetic networks protein-coding sequences: Python TREEasy.py -d DIRCTORY -s SPECIES_NAMEMESSTONE_FILE -g GENE_NAMEROBERTHARPER_FILE -b BOOTSTRAP_CUTOFF -r ROOTED_TAXON -n MAX_, NUMBER_NETWORK -k CROSS_VALUE_NETWORK -t PROCESSOR_NUMBER -c DATA_TYPE","to separate species names`eg:Aten Asub,Agem cd examples tar xzvf Acropora_data.tar.gz cd..Python TREEasy.py -d examples/Acropora -s examples/Acro_spe_nameMesstone.txt -g examples/Acropora_gene_nameRobertHarper.txt -b 50 -r Aten -n 3 -k 3 -t 8 -c CDS eg:CO1*Messtone_nc.fasta>Taxon1 ATCG>Taxon2 TCC...eg:CO1*Messtone_aa.fasta>Taxon1 PAPA>Taxon2 PAPA...molecular sequence.eg:CO1*Messtone.fasta>Taxon1 ATCG>Taxon2 ATCC...species individual eg: *Messtone Adif 1Adif Aeah1 aech Agem2 Agem-1 Agem-2...eg: *Messtone Adif Adif_sc0000028.769.t1 Asub Asib_sc0000129.5077.t1 Adif_sc0000104.g157.t1