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reactome / analysis-core

Pathway enrichment and expression analysis as well as species comparison tool
https://reactome.org/dev/analysis
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Analysis Core

What is Reactome Analysis Core?

Reactome Analysis Core creates the analysis intermediate file and it is also used as part of the AnalysisService (as a dependency).

Creating The Analysis Intermediate File

To create the intermediate binary file, the command is as follows:

:warning: Before creating the intermediate file, make sure this query MATCH (n:DBInfo) RETURN n returns reactome

java -jar analysis-core-exec.jar \
      -h graph_db_host \
      -p graph_db_port \
      -u graph_db_user \
      -k graph_db_passwd \
      -o pathTO/analysis_vXX.bin

Add --verbose to see the building status on the screen.

Please note XX refers to the current Reactome release number. The analysis_vXX.bin file has to be copied in the corresponding "AnalysisService/input/" folder and then change the symlink of analysis.bin in that folder to point to the new file.

Once the AnalysisService is restarted the new data will be used.

Recommendation

It is recommended to specify the initial and maximum memory allocation pool for the Java Virtual Machine

-Xms2048M -Xmx5120M