MetFrag relaunched

Requirements

• Java = openjdk11
• Apache Maven = 3.8

Sources

• download sources by cloning git repository
  

git clone https://github.com/ipb-halle/MetFragRelaunched.git

MetFrag Webapp container

This container packages the MetFrag (https://github.com/ipb-halle/MetFragRelaunched) webapp and some text databases based on the latest official tomcat docker container.

Following options are supported:

• environment variable JAVA_OPTS="-Xmx?g -Xms?g" to adjust jvm memory
• environment variable WEBPREFIX to adjust the web app name
• automatic use of a metfrag settings file if provided at /resources/settings.properties

Examples:

Run MetFrag at http://localhost:8888/MetFragWeb

docker run -it --rm -p 8888:8080 ipb-halle/metfragweb

Run Metfrag at http://localhost:8888/mymetfrag with 4GB JVM size using a settings file from ./settings.properties

docker run -it --rm -e  JAVA_OPTS="-Xmx4g -Xms4g" -e WEBPREFIX=mymetfrag -v $(pwd)/settings.properties:/resources/settings.properties -p 8888:8080 ipbhalle/metfragweb

Container repositories

See https://hub.docker.com/r/ipbhalle/metfragweb for automatic builds.

MetFragLib

Build

mvn clean install -pl MetFragLib -am

• skipping test during build by
  

mvn clean install -pl MetFragLib -am -DskipTests

MetFragCommandLine

Basics

• MetFrag commandline version depends on MetFragLib
• for a short tutorial visit http://ipb-halle.github.io/MetFrag/projects/metfragcl/

Build

mvn clean install -pl MetFragCommandLine -am

• skipping test during build by
  

mvn clean install -pl MetFragCommandLine -am -DskipTests

MetFragR

Basics

• MetFrag R package depends on MetFragLib
  
• for a short tutorial visit http://ipb-halle.github.io/MetFrag/projects/metfragr/

Build

mvn clean install -pl MetFragR -am

• skipping test during build by
  

mvn clean install -pl MetFragR -am -DskipTests

• after the successful build the MetFragR java library is located in MetFragR/rpackage/metfRag/inst/java/
• point to the directory MetFragR/rpackage/ to perform checks and the build of the R package
  

R CMD check metfRag
R CMD build metfRag

• after the successful build the R package can be installed in R
  

install.packages("metfRag",repos=NULL,type="source")
library(metfRag)

• all earlier steps can be skipped by installing the pre-compiled R package from GitHub
  

library(devtools)
install_github("ipb-halle/MetFragR/metfRag")

MetFragWeb

Basics

• MetFrag web version depends on MetFragLib. Runs with Java Server Faces 2.2 and PrimeFaces 5.3 and brings its own Tomcat web server
  

Configuration

• rename file settings.properties.template in MetFragWeb/src/main/webapp/resources to settings.properties and set necessary parameters
  

## define chemspider token to query ChemSpider database
ChemSpiderToken = ...

## if MetFragWeb host is connected via proxy to the internet provide proxy settings for 
## different web services
MoNAProxyServer = ...
MoNAProxyPort = ...

KeggProxyServer = ...
KeggProxyPort = ...

MetaCycProxyServer = ...
MetaCycProxyPort = ...

## to speed up database queries you can set up local repositories by setting up MySQL or 
## PostgreSQL databases
LocalPubChemDatabase = ...
LocalPubChemDatabaseCompoundsTable = ...
LocalPubChemDatabasePortNumber = ...
LocalPubChemDatabaseServerIp = ...
LocalPubChemDatabaseMassColumn = ...
LocalPubChemDatabaseFormulaColumn = ...
LocalPubChemDatabaseInChIColumn = ...
LocalPubChemDatabaseInChIKey1Column = ...
LocalPubChemDatabaseInChIKey2Column = ...
LocalPubChemDatabaseCidColumn = ...
LocalPubChemDatabaseSmilesColumn = ...
LocalPubChemDatabaseUser = ...
LocalPubChemDatabasePassword = ...
LocalPubChemDatabaseCompoundNameColumn = ...

Build and Run

mvn clean install -pl MetFragWeb -am
mvn org.codehaus.cargo:cargo-maven3-plugin:run -pl MetFragWeb

• skipping test during build by
  

mvn clean install -pl MetFragWeb -am -DskipTests
mvn org.codehaus.cargo:cargo-maven3-plugin:run -pl MetFragWeb

• after the successful build Tomcat web server runs on port 8080
  
• MetFragWeb can be accessed via pointing to http://localhost:8080/index.xhtml in the web browser
  

Build

• if you just want to build the war file to transfer it to another Tomcat instance, run:

mvn clean package -pl MetFragWeb -am

• after the successful build the war file is located in MetFragWeb/target/MetFragWeb.war

Additionals

Run main methods

mvn exec:java -Dexec.mainClass="java_class_path" -Dexec.args="arg0 arg1 arg2 ..."  

References

Ruttkies C., Schymanski E.L. et al, MetFrag relaunched: incorporating strategies beyond in silico fragmentation. Journal of Cheminformatics, 2016, 8:3. http://jcheminf.springeropen.com/articles/10.1186/s13321-016-0115-9