Hi there,

I'm getting exactly the same problem with any job running on a TORQUE/PBS
cluster. The jobs actually run fine as I can see the output and download
it, but it's marked as failed in the galaxy history, with the following
message:

WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako)
cannot be fetched

The command `python -ES ./scripts/fetch_eggs.py` gives nothing as output.
If I run the same tools locally there is no problem.

Cheers
Micka


> Message: 5
> Date: Thu, 27 Oct 2011 15:08:17 +1100
> From: Jerico Nico De Leon Revote <jerico.rev...@monash.edu>
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] Local Galaxy Instance MarkupSafe error
> Message-ID:
>        <cap9ulhyipxyb2cwtqosm3mquuu55arxy5por1dbahej1uco...@mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> I'm just doing a simple get->data from UCSC on our local Galaxy
> instance and got the following error:
>
> WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako)
> cannot be fetched
>
> The job box then is displayed as red on the history panel.
> The job runner states that the job finished normally on the cluster.
> Galaxy is checkout from galaxy-central (changeset: 6176:34fffbf01183).
>
> Thanks,
>
> Jerico
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> ------------------------------
>
> Message: 6
> Date: Thu, 27 Oct 2011 16:58:13 +1100
> From: Jerico Nico De Leon Revote <jerico.rev...@monash.edu>
> To: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error
> Message-ID:
>        <cap9ulhbenenkqc50uzyxoca4w-zucdy8obs4i6b3e2qyfmy...@mail.gmail.com
> >
> Content-Type: text/plain; charset="iso-8859-1"
>
> Just to follow-up on this. The MarkupSafe egg is definitely present on the
> eggs directory and the servers are ran through virtualenv.
>
> On 27 October 2011 15:08, Jerico Nico De Leon Revote <
> jerico.rev...@monash.edu> wrote:
>
> > Hi,
> >
> > I'm just doing a simple get->data from UCSC on our local Galaxy instance
> and got the following error:
> >
> > WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako) cannot
> be fetched
> >
> > The job box then is displayed as red on the history panel.
> > The job runner states that the job finished normally on the cluster.
> > Galaxy is checkout from galaxy-central (changeset: 6176:34fffbf01183).
> >
> > Thanks,
> >
> > Jerico
> >
> >
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> >
>
> ------------------------------
>
> Message: 7
> Date: Thu, 27 Oct 2011 02:40:51 -0400
> From: Nate Coraor <n...@bx.psu.edu>
> To: Jerico Nico De Leon Revote <jerico.rev...@monash.edu>
> Cc: galaxy-dev@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error
> Message-ID: <20111027064051.gg2...@bx.psu.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Jerico Nico De Leon Revote wrote:
> > Hi,
> >
> > I'm just doing a simple get->data from UCSC on our local Galaxy
> > instance and got the following error:
> >
> > WARNING:galaxy.eggs:Warning: MarkupSafe (a dependent egg of Mako)
> > cannot be fetched
> >
> > The job box then is displayed as red on the history panel.
> > The job runner states that the job finished normally on the cluster.
> > Galaxy is checkout from galaxy-central (changeset: 6176:34fffbf01183).
>
> Hi Jerico,
>
> Are you using a cluster?  If not, could you run:
>
>    % python -ES ./scripts/fetch_eggs.py
>
> --nate
>
> >
> > Thanks,
> >
> > Jerico
>
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
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>
> --
Mickael Escudero, Bioinformatics Officer
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