From Glen.Beane@jax.org Wed Dec  1 11:08:07 2010
From: Glen Beane <Glen.Beane@jax.org>
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] lastz_seqs data table; error preparing job
Date: Wed, 01 Dec 2010 11:07:57 -0500
Message-ID: <5E59D00C-9356-4393-8F2B-C24E66089E5F@jax.org>
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I just updated my local Galaxy install to the latest galaxy-dist.  The lastz =
tool seems to have been changed so it needs a lastz_seqs data table.=20

I added (as a guess)

    <table name=3D"lastz_seqs">
        <columns>name, value</columns>
        <file path=3D"tool-data/lastz_seqs.loc" />
    </table>


to tool_data_table_conf.xml.


the lastz tool will now load, and it shows my reference sequences in the drop=
 down list.  However, now when I run lastz I get an error while it is trying =
to setup the job:

Traceback (most recent call last):
  File "/galaxydata/galaxy-setup/galaxy-dist/lib/galaxy/jobs/runners/pbs.py",=
 line 186, in queue_job
    job_wrapper.prepare()
  File "/galaxydata/galaxy-setup/galaxy-dist/lib/galaxy/jobs/__init__.py", li=
ne 368, in prepare
    self.command_line =3D self.tool.build_command_line( param_dict )
  File "/galaxydata/galaxy-setup/galaxy-dist/lib/galaxy/tools/__init__.py", l=
ine 1524, in build_command_line
    command_line =3D fill_template( self.command, context=3Dparam_dict )
  File "/galaxydata/galaxy-setup/galaxy-dist/lib/galaxy/util/template.py", li=
ne 9, in fill_template
    return str( Template( source=3Dtemplate_text, searchList=3D[context] ) )
  File "/galaxydata/galaxy-setup/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-linux-x=
86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__
    return getattr(self, mainMethName)()
  File "DynamicallyCompiledCheetahTemplate.py", line 119, in respond
IndexError: list index out of range





--
Glen L. Beane
Software Engineer
The Jackson Laboratory
Phone (207) 288-6153





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From Glen.Beane@jax.org Wed Dec  1 11:25:12 2010
From: Glen Beane <Glen.Beane@jax.org>
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] lastz_seqs data table; error preparing job
Date: Wed, 01 Dec 2010 11:25:02 -0500
Message-ID: <286E5CB6-41E6-41E6-93C9-AD8D7B8CD2C2@jax.org>
In-Reply-To: <5E59D00C-9356-4393-8F2B-C24E66089E5F@jax.org>
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On Dec 1, 2010, at 11:07 AM, Glen Beane wrote:

> I just updated my local Galaxy install to the latest galaxy-dist.  The last=
z tool seems to have been changed so it needs a lastz_seqs data table.=20
>=20
> I added (as a guess)
>=20
>    <table name=3D"lastz_seqs">
>        <columns>name, value</columns>
>        <file path=3D"tool-data/lastz_seqs.loc" />
>    </table>
>=20



oh, I just noticed the lastz_seqs.loc.sample file now has three columns.  I g=
uess I should have taken a look at that first!


--
Glen L. Beane
Software Engineer
The Jackson Laboratory
Phone (207) 288-6153





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