Hi Nate,
Yes, that was the issue. I just made sure that the cluster nodes are using the same Python as the application server and it works now.
Thanks for the support.
Regards,
Jerico
Jerico Nico De Leon Revote wrote:
> It's the same case as what I'm getting. I can see the output via "eye" iconDo your cluster nodes have internet access? If so, log into a node and
> on the history panel and able to download the files as well.
run the command again from there. Your nodes may have a different
Python version or Unicode byte order encoding scheme than your Galaxy
application server.
--nate
>
> On 1 November 2011 03:37, Mickael ESCUDERO <mickael.escudero@gmail.com>wrote:
>
> > 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>
> >> 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
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >> URL: <
> >> http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20111027/cd777ff3/attachment-0001.html
> >> >
> >>
> >> ------------------------------
> >>
> >> 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>
> >> 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.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
> >> >
> >> >
> >> -------------- next part --------------
> >> An HTML attachment was scrubbed...
> >> URL: <
> >> http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20111027/f8baadf6/attachment-0001.html
> >> >
> >>
> >> ------------------------------
> >>
> >> 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
> >>
> >> > ___________________________________________________________
> >> > Please keep all replies on the list by using "reply all"
> >> > in your mail client. To manage your subscriptions to this
> >> > and other Galaxy lists, please use the interface at:
> >> >
> >> > http://lists.bx.psu.edu/
> >>
> >> --
> > Mickael Escudero, Bioinformatics Officer
> >
> >
> > ___________________________________________________________
> > Please keep all replies on the list by using "reply all"
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> >
> > http://lists.bx.psu.edu/
> >
> ___________________________________________________________
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