From dannonbaker@me.com Mon Dec  6 11:47:49 2010
From: Dannon Baker <dannonbaker@me.com>
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Error setting-up and running bowtie tasks
Date: Mon, 06 Dec 2010 11:47:17 -0500
Message-ID: <5B9714C9-D4CF-4D35-87B8-8B37A02969BF@me.com>
In-Reply-To: <4CFD123E.7090209@compbio.dundee.ac.uk>
MIME-Version: 1.0
Content-Type: multipart/mixed; boundary="===============7680790755490722966=="

--===============7680790755490722966==
Content-Type: text/plain; charset="utf-8"
Content-Transfer-Encoding: quoted-printable

Thanks for catching this.  Fixed in galaxy-central.

-Dannon

On Dec 6, 2010, at 11:41 AM, Chris Cole wrote:

> Oh, and I should also add there was a small bug in the error output:
>=20
> galaxy.jobs.runners.drmaa ERROR 2010-12-06 14:39:51,555 Uncaught exception =
queueing job
> Traceback (most recent call last):
>  File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py", li=
ne 112, in run_next
>    self.queue_job( obj )
>  File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py", li=
ne 128, in queue_job
>    log.exception("failure running job %d" % job_wrapper.get_id_tag())
> TypeError: %d format: a number is required, not str
>=20
> THis is fixable by changing the below:
> diff -r 8a4ff7b2c6e6 lib/galaxy/jobs/runners/drmaa.py
> --- a/lib/galaxy/jobs/runners/drmaa.py  Tue Nov 30 13:05:42 2010 +0000
> +++ b/lib/galaxy/jobs/runners/drmaa.py  Mon Dec 06 14:47:45 2010 +0000
> @@ -125,7 +125,7 @@ class DRMAAJobRunner( BaseJobRunner ):
>             command_line =3D self.build_command_line( job_wrapper, include_=
metadata=3DTrue )
>         except:
>             job_wrapper.fail( "failure preparing job", exception=3DTrue )
> -            log.exception("failure running job %d" % job_wrapper.get_id_ta=
g())
> +            log.exception("failure running job %s" % job_wrapper.get_id_ta=
g())
>             return
>=20
>         runner_url =3D job_wrapper.tool.job_runner
>=20
>=20
> On 06/12/10 15:30, Kelly Vincent wrote:
>> Chris,
>>=20
>> The tool_data_table_conf.xml.sample file has been updated to the correct
>> column values, so just copy that or the relevant sections over. Let us
>> know if you have any problems getting things working.
>>=20
>> Regards,
>> Kelly
>>=20
>>=20
>> On Dec 6, 2010, at 10:20 AM, Chris Cole wrote:
>>=20
>>> I have previously been able to run bowtie jobs successfully, but now I
>>> get this error:
>>> galaxy.jobs.runners.drmaa ERROR 2010-12-06 15:09:44,068 failure
>>> running job 2248
>>> Traceback (most recent call last):
>>> File
>>> "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py",
>>> line 124, in queue_job
>>> job_wrapper.prepare()
>>> File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/__init__.py",
>>> line 368, in prepare
>>> self.command_line =3D self.tool.build_command_line( param_dict )
>>> File "/homes/www-galaxy/galaxy_devel/lib/galaxy/tools/__init__.py",
>>> line 1524, in build_command_line
>>> command_line =3D fill_template( self.command, context=3Dparam_dict )
>>> File "/homes/www-galaxy/galaxy_devel/lib/galaxy/util/template.py",
>>> line 9, in fill_template
>>> return str( Template( source=3Dtemplate_text, searchList=3D[context] ) )
>>> File
>>> "/homes/www-galaxy/galaxy_devel/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs=
2.egg/Cheetah/Template.py",
>>> line 1004, in __str__
>>> return getattr(self, mainMethName)()
>>> File "DynamicallyCompiledCheetahTemplate.py", line 182, in respond
>>> IndexError: list index out of range
>>>=20
>>> I've a feeling it has something to with the bowtie_indices.loc file
>>> and it's associated entry in tool_data_table_conf.xml. I can see that
>>> the format for the .loc file has changed (it now has four columns
>>> instead of two):
>>> h_sapiens37 NCBI37 Homo sapiens ncbi37 /db/bowtie/h_sapiens_37_asm
>>>=20
>>> But the xml doesn't match (it only has two columns):
>>>=20
>>> <!-- Locations of indexes in the Bowtie mapper format -->
>>> <table name=3D"bowtie_indexes">
>>> <columns>name, value</columns>
>>> <file path=3D"tool-data/bowtie_indices.loc" />
>>> </table>
>>>=20
>>> What should there be in the 'columns' section?
>>> Thanks,
>>>=20
>>> Chris
>>> _______________________________________________
>>> galaxy-dev mailing list
>>> galaxy-dev(a)lists.bx.psu.edu
>>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>>=20
>=20
>=20
> --=20
> Dr Chris Cole
> Senior Bioinformatics Research Officer
> School of Life Sciences Research
> University of Dundee
> Dow Street
> Dundee
> DD1 5EH
> Scotland, UK
>=20
> url: http://network.nature.com/profile/drchriscole
> e-mail: chris(a)compbio.dundee.ac.uk
> Tel: +44 (0)1382 388 721
>=20
> The University of Dundee is a registered Scottish charity, No: SC015096
> _______________________________________________
> galaxy-dev mailing list
> galaxy-dev(a)lists.bx.psu.edu
> http://lists.bx.psu.edu/listinfo/galaxy-dev


--===============7680790755490722966==--