Re: [galaxy-dev] Galaxy not recording return codes (error levels)

2012-09-21 Thread Paul Gordon
Somewhat related, can I make a feature request that in the job attribute editor screen (i.e. what you get when you click the pencil icon in the top right corner of a history item), you can manually change the state of a job from failed (which means you can't use the output in any subsequent

Re: [galaxy-dev] re-writing username for login or stripping domain from remote_user?

2012-07-18 Thread Paul Gordon
IANAAG, but the following should be secure and effective as well (at least it works for me), setting REMOTE_USER with an Apache authentication module in conjunction with ProxyPass RequestHeader set REMOTE_USER %{REMOTE_USER}s RequestHeader edit REMOTE_USER ^.*(.+?) $1 Cheers, Paul On

Re: [galaxy-dev] Sub-task splitting

2012-05-03 Thread Paul Gordon
+1. This is especially useful for us, with hardware-accelerated algorithms having limits on input size. On 12-05-03 9:51 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hello all, Currently the Galaxy experimental task splitting code allows splitting into N chunks, e.g. 8 parts, with:

[galaxy-dev] Galaxy workflow data

2012-02-14 Thread Paul Gordon
Hi all, I have noticed that when I run a workflow with output to a new history, the data sets used as input to the workflow do not become part of the new history. Unfortunately, if a job fails in the workflow, the rerun interface for the job can't access the original dataŠit needs to be manually

[galaxy-dev] Shared Data as options for tools

2012-02-02 Thread Paul Gordon
Hi all, Is there a way, or better yet a coded example, of how to list the options for an input parameter using the contents of a shared data library? Up until now I've use Python scripts to get the input file options from a directory listing for a hardcoded path on the server, but it'd be much

Re: [galaxy-dev] naming of history steps

2012-02-01 Thread Paul Gordon
+1 votes :-) This would also give graph generating tools a fighting chance to present something useful in any graphs generated. E.g. GC Bias Plot of Solid 24A could have a title of Solid 24A instead of dataset_234.dat What do you think of this first-last model?

Re: [galaxy-dev] disk space and file formats

2011-09-03 Thread Paul Gordon
adoption beyond PacBio, but I have seen some things popping up in Galaxy. FWIW, the XSQ format files created by the 5500 Series ABI SOLiD are HDF5, but not BioHDF: http://solidsoftwaretools.com/gf/download/docmanfileversion/309/1079/XSQ_Webinar_20110215.pdf -- __ Paul Gordon

Re: [galaxy-dev] Apache configuration problem

2011-08-02 Thread Paul Gordon
. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- __ Paul Gordon Bioinformatics Support Specialist Alberta Children's Hospital Research Institute http://www.ucalgary.ca/~gordonp