set Qualimap RAM memory usage size once instead of every-time at launch

[xiaol...@gmail.com]

Dear Qualimap users,

Is there a way to set Qualimap RAM memory usage size once instead of every time at lanching Qualimap? I have 64 GB of memory installed but Qualimap still fails at RNA-Seq QC with the error of "running out of memory".  I have to launch from the command line (I used to just double click the "Qualimap" icon to launch it) with "./qualimap --java-mem-size=10000M", and then it runs ok. Is there a way to set 10000M as the default RAM usage size for Qualimap so that I do not have to do this every time at launching?

Thanks,

Xiao

[Konstantin Okonechnikov]

Hi Xiao,

the default limit for RAM could be easily assigned by several ways. 

First it could be manually edited in the command qualimap (https://bitbucket.org/kokonech/qualimap/src/master/cli/qualimap), the variable to edit is in line 7  :

JAVA_MEM_DEFAULT_SIZE="1200M"

simply change it to the desired 10000M or 10G.

Second, you could assign a variable JAVA_OPTS in the system, and then it would be used by default. Here's example overview: 

https://stackoverflow.com/questions/10003459/java-opts-for-increasing-heap-size

Best regards,

  Konstantin

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[Xiao Lei]

Hi, Konstantin,

Thank you very much for your help. I followed your instruction the line 7 in Qualimap script and it worked. 

Best,

Xiao

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