You can create multiple variants of the 10G_memory tool with different native specifications right? Does this work around result in too much XML? Dynamic destinations could also be used - if you are interested I could post a demo rule that you might be able to use.
The memory card referenced above might help, but a much easier cards might help this would be... https://trello.com/c/t1FH1Q5P Also tool style macros for job_conf.xml might help right - keep size of XML down? https://trello.com/c/wt1LflNh Feel free to create another card for this request (allowing parameterized tools to influence destination parameters) - seems reasonable. -John On Tue, Apr 22, 2014 at 1:32 PM, Björn Grüning <bjoern.gruen...@gmail.com> wrote: > Hi, > > to specify -Xmx and -Xms for java based programs I set my preferred values > to $_JAVA_OPTIONS and include _JAVA_OPTIONS as nativeSpecification with -v > _JAVA_OPTIONS. That worked good so far, but the downside is that I can not > have different options for different tools. Is there a trick I can specify > arbitrary $ENVs to a specific tool? Any ideas how to solve that, without > hacking the -Xmx and -Xms parameters into the wrapper file? > > It is related to https://trello.com/c/HGEYPQf6. > I would be interested in workarounds until that card is closed :) > > Something like that would be great: > <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gatk2/gatk2_indel_realigner" > destination="10G_memory"> > <param id="nativeParam">export _JAVA_OPTIONS='-Xmx=6GB'</param> > </tool> > > Thanks! > Bjoern > > > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
