Hi John and Nicola
Thank you very much for working on this and presenting a solution so fast!
Hans-Rudolf
PS: https://github.com/galaxyproject/galaxy/pull/2800
On 08/16/2016 04:40 PM, John Chilton wrote:
Yup - thanks for the bug report. I have used your rna example to build a minimal-ish example to fit into Galaxy's test tools framework here https://github.com/galaxyproject/galaxy/pull/2795. I also tested in 16.01 and it worked - so this clearly broke in 16.04. I'll see if I can track it down and we can move the discussion to the github PR. Thanks a bunch for the detailed report Hans!
-John
On Tue, Aug 16, 2016 at 9:02 AM, Hans-Rudolf Hotz hrh@fmi.ch wrote:
Hi Nicola and others on the list
It looks like it has something to do with the 'conditional'
I took the rnaStar xml file, and reduced it to the bare bones, just to reproduce the issue (see attachment: rg_rnaStar.simple ). This works. It picks up the right dbkey.
I made the xml file even simpler and removed the 'conditional' (see attachment: rg_rnaStar.simple_noCond ). And now it no longer works (see attached screenshot)
And just for completeness: There is nothing in the logs
However, if I use the same two xml files on our current galaxy servers (running 15.10). It works in both cases. Each time, the right dbkey is picked up.
Hans-Rudolf
On 08/16/2016 01:47 PM, Hans-Rudolf Hotz wrote:
Hi Nicola
Many thanks for your comments/suggestions. I've just tested the rnaStar wrapper, and it works as well.
I will try to dig deeper
Hans-Rudolf
On 08/16/2016 01:38 PM, Nicola Soranzo wrote:
I've tested bowtie_wrapper on Galaxy release_16.04: <option type="from_data_table" name="bowtie_indexes" column="1" offset="0"> works fine for me.
Cheers, Nicola
On 16/08/16 11:42, Nicola Soranzo wrote:
Forget about my previous comment, I should have read your email better, sorry!
Your code similar to bowtie_wrapper is also used by
https://github.com/galaxyproject/tools-iuc/blob/master/tools/rgrnastar/rg_rn...
and I think it should work, not sure if it's a regression in Galaxy.
Cheers, Nicola
On 16/08/16 11:29, Nicola Soranzo wrote:
Hi Hans, see my comment below.
On 16/08/16 09:51, Hans-Rudolf Hotz wrote: > > Dear All > > > I am trying to move our Galaxy installation to new hardware and at > the same time to a new version (the original is "15.10",minor > version "2" via mercurial; the new is "16.04" via github): > > So far, I am making good progress, but I am struggling with a tool > which was written by someone else who has left more than 2 years > ago. The problem is: it doesn't set the dbkey correctly. > > I get: > <Cheetah.Template.Template object at 0x7f1e40210f50> > > > > The tool xml is as follows: > > <inputs> > <param name="sample_file" type="data" > format="qsamples,qsamplespaired" label="Sample File" help="set of > sequence files created by the 'select sequence files' tool"> > </param> > <param name="index" type="select" label="Reference Genome" > help="all reads will be mapped to this reference"> > <options from_data_table="fmi__quasr_genomes"/> > </param> > > ... > </inputs> > <outputs> > <data name="output01" type="data" format="qproject" > label="qProject of ${sample_file.name}"> > <actions> > <action type="metadata" name="dbkey"> > <option type="from_param" name="index"/>
It seems you are missing a param_attribute="dbkey" here, it should be:
<option type="from_param" name="index" param_attribute="dbkey"/>
Cheers, Nicola
> </action> > </actions> > </data> > </outputs> > > > > The user can select a genome (based on the Bioconductor BSgenome > packages) from the tab delimited fmi__quasr_genomes table, which > looks like: > > hg19BSg hg19BSg BSgenome Hsapiens (UCSC hg19) > BSgenome.Hsapiens.UCSC.hg19 > hg18BSg hg18BSg BSgenome Hsapiens (UCSC hg18) > BSgenome.Hsapiens.UCSC.hg18 > ce10BSg ce10BSg BSgenome Celegans (UCSC ce10) > BSgenome.Celegans.UCSC.ce10 > ce6BSg ce6BSg BSgenome Celegans (UCSC ce6) > BSgenome.Celegans.UCSC.ce6 > ... > > > The tool works: > - it displays the available genomes (BSgenome Hsapiens (UCSC hg19), > hg18BSg hg18BSg BSgenome Hsapiens (UCSC hg18), etc) > - once the job is submitted, it uses the right Bioconductor package > (BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg18, etc) > > However, instead of the dbkey (hg19BSg, hg18BSg, etc) I get: > <Cheetah.Template.Template object at 0x7f1e40210f50> > > > > Has anything changed with the 'action' tag since release 15.10? > which makes this simple xml no longer working? > > I have to admit, it does look different than the example on the wiki > > (https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cactions.3E_t... > > ). I tried the code from the wiki which is based on the > bowtie_wrapper > > (https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie_wrap...) > > as well: > > > <actions> > <action type="metadata" name="dbkey"> > <option type="from_data_table" name="fmi__quasr_genomes" > column="1" offset="0"> > <filter type="param_value" column="0" value="#" > compare="startswith" keep="False"/> > <filter type="param_value" ref="index" column="0"/> > </option> > </action> > </actions> > > > but it results in the same kind of error: > <Cheetah.Template.Template object at 0x7ff82c0e43d0> > > > Thank you very much for any help/comments > > Regards, Hans-Rudolf > > > > > > >
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