Hi Nate,

It must be the issue here, I just learnt the head node is running with redhat 5 while Galaxy and all the dependencies are running on a redhat 6 server so yes the python version is not the same.
I'll see what I can do with my IS department then.

Cheers for the help :)

Micka


On 2 November 2011 17:18, Nate Coraor <nate@bx.psu.edu> wrote:
Jerico Nico De Leon Revote wrote:
> It's the same case as what I'm getting. I can see the output via "eye" icon
> on the history panel and able to download the files as well.

Do your cluster nodes have internet access?  If so, log into a node and
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"
> > in your mail client.  To manage your subscriptions to this
> > and other Galaxy lists, please use the interface at:
> >
> >  http://lists.bx.psu.edu/
> >

> ___________________________________________________________
> 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