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.laza...@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.burr...@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 <d...@bx.psu.edu> >> >> date: Sun Sep 25 13:27:14 2011 -0400 >> >> summary: Some random lines tool tweaks. >> >> >> >> Thank you for your assistance. >> >> >> >> Michael. >> >> >> >> ________________________________ >> Please note, that my email address is no longer >> givenname.surn...@bbsrc.ac.uk. Please update your records to reflect my new >> email address of givenname.surn...@nbi.ac.uk as shown on this email. >> ___________________________________________________________ >> 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/ >> > > > > -- > 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; ___________________________________________________________ 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/
