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:

<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 name="index" type="select" label="Reference Genome" help="all reads will be mapped to this reference">
      <options from_data_table="fmi__quasr_genomes"/>

<data name="output01" type="data" format="qproject" label="qProject of ${}">
         <action type="metadata" name="dbkey">
            <option type="from_param" name="index"/>

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 ( ). I tried the code from the wiki which is based on the bowtie_wrapper ( as well:

        <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"/>

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


Hans-Rudolf Hotz, PhD
Bioinformatics Support

Friedrich Miescher Institute for Biomedical Research
Maulbeerstrasse 66
4058 Basel/Switzerland
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