No substantiation error for java.

Magda Orzechowska

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Oct 30, 2017, 9:07:28 AM10/30/17

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Dear Colleagues,

We maintain Gene Paterrn in form of our lab server and recently with the latest update of GP we started to experience the followed error (stderr):

HierarchicalClustering: no substitution available for  in command line <java> <java_flags> -Djava.awt.headless=true -Dlibdir=<libdir> -Dwin=cluster.exe -Dmac=clusterMac -Dlinux=clusterLinux -Dlinux64=clusterLinux64 -cp <libdir>hcl.jar<path.separator><libdir>legacy-gp-modules.jar<path.separator><libdir>ant.jar org.genepattern.modules.hcl.RunCluster -f <input.filename> <log.transform> <row.center> <row.normalize> <column.center> <column.normalize> -u <output.base.name> -e <column.distance.measure> -g <row.distance.measure> -m <clustering.method>.

This issue was not present when we had older GP version, however with older version of GP we were not able to use new Viewer app, because it could not reach our server.

We will appreciate any help how to solve this issue. In addition, our server is working under Linux.

Best regards!

Peter Carr

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Oct 30, 2017, 9:26:01 AM10/30/17

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You need to set the following substitution variables:
java=
java_flags=

In your custom.properties file.

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Peter Carr
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Broad Institute (http://broadinstitute.org) - GenePattern Team (http://genepattern.org/)

Joris VAN HOUTVEN

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Feb 13, 2019, 5:19:53 AM2/13/19

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Hi Peter

This works for perl, but for some strange reason it didn't work for python (or rather, 'python_3.6'). I have set:

  python_3.6=/usr/bin/python3
  python3=/usr/bin/python3
  python=/usr/bin/python3

but none of them work. Any ideas?

Op maandag 30 oktober 2017 14:26:01 UTC+1 schreef Peter Carr:

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