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 <n...@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.escud...@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.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
> > >> -------------- 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.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
> > >> >
> > >> >
> > >> -------------- 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 <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"
> > >> > 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
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