A fix for these warnings is in revision 6048 of galaxy-central - again, thanks for pointing them out Michael. For the record, the warnings were from the HSmetrics and GCbias tools and arose because there is a user configurable maxheap parameter that is not available by default - it is commented out in the tool form - but it had not been commented out from the test - since it is not enabled by default that generated a warning. The test parameter is now also commented out by default and must be uncommented for sites running into ram limits with very large datasets. On Tue, Sep 27, 2011 at 8:04 AM, Ross <ross.lazarus@gmail.com> wrote:
Michael,
Thanks for pointing these warning errors out. I think they're harmless and can be ignored but I'll definitely take a look later today and check in a fix. As I recall, we had some discussion some months ago about whether to allow the user to set the size of the java heap and decided that it was not necessary - these messages suggest the parameter is still somewhere in the tool tests - oddly enough I can't see it but I'm seeing the same messages! I'll let you know what I find once I've had a chance to take a look.
On Mon, Sep 26, 2011 at 11:06 PM, michael burrell (TOC) <michael.burrell@nbi.ac.uk> wrote:
Good afternoon,
When starting galaxy I find the following errors logged in the paster.log
galaxy.tools DEBUG 2011-09-26 13:58:21,577 Loaded tool: PicardASMetrics 0.03
galaxy.tools.test DEBUG 2011-09-26 13:58:21,625 Error in add_param for maxheap: Unable to determine parameter type of test input 'maxheap'. Ensure that the parameter exists and that any container groups are defined first.
galaxy.tools DEBUG 2011-09-26 13:58:21,703 Loaded tool: PicardInsertSize 0.3.0
galaxy.tools.test DEBUG 2011-09-26 13:58:21,737 Error in add_param for maxheap: Unable to determine parameter type of test input 'maxheap'. Ensure that the parameter exists and that any container groups are defined first.
Our galaxy version is.
galaxy@jic55666:~/software/galaxy-central$ hg tip
changeset: 6042:2469c53051ea
tag: tip
user: Daniel Blankenberg <dan@bx.psu.edu>
date: Sun Sep 25 13:27:14 2011 -0400
summary: Some random lines tool tweaks.
Thank you for your assistance.
Michael.
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-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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Ross