Wondering if anyone has reported this for the doc/sample file team: Isn't the java config example line in that file wrong (at least for my java 1.6):
<env id="_JAVA_OPTIONS">-Xmx=6GB</env> With a setting of -Xmx=10g, Picard wouldn't run sortSam, instead this stderr text: ***************** Fatal error: Exit code 1 () Picked up _JAVA_OPTIONS: -Xmx=10g Invalid maximum heap size: -Xmx=10g Could not create the Java virtual machine. ***************** I changed the <env> tag to take out "=" so it reads: <env id="_JAVA_OPTIONS">-Xmx6G</env> and now its working fine! Had to lookup -Xmx param format on the net from: http://javahowto.blogspot.ca/2006/06/6-common-errors-in-setting-java-heap.html Regards, Damion. Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___________________________________________________________ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
