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 <[email protected]> > To: [email protected] > 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 <[email protected]> > To: [email protected] > 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 < > [email protected]> 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 <[email protected]> > To: Jerico Nico De Leon Revote <[email protected]> > Cc: [email protected] > Subject: Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error > Message-ID: <[email protected]> > 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
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