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.revote@monash.edu>
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] Local Galaxy Instance MarkupSafe error
Message-ID:
<CAP9ULhYiPxYB2CWtqOSM3MquUu55ARxY5poR1dBaHEj1UcO8UQ@mail.gmail.com>
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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.revote@monash.edu>
To: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error
Message-ID:
<CAP9ULhbeNeNKQc50UZyXoCA4w-zuCDy8OBS4i6b3e2QyfMy3Dg@mail.gmail.com>
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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.revote@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 <nate@bx.psu.edu>
To: Jerico Nico De Leon Revote <jerico.revote@monash.edu>
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error
Message-ID: <20111027064051.GG2102@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
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