Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-11-02 Thread Jerico Nico De Leon Revote 
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

On 3 November 2011 04:18, 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
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   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
   
   
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   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
  
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[galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-10-26 Thread Jerico Nico De Leon Revote 
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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Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-10-26 Thread Jerico Nico De Leon Revote 
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


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[galaxy-dev] Error in displaying data in galaxy browser with less than 1MB size.

2011-09-15 Thread Jerico Nico De Leon Revote 
Hi,

I've a setup a local instance of galaxy in our server using
PostgreSQL/nginx.
I've followed the instructions from the production server configuration as
stated from here:

http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server.

Galaxy is running and tried the Galaxy 101 tutorial but I get http 404
error when trying to view any dataset with less than 1MB in size in the
galaxy browser:
Not Found

The resource could not be found.
No route for
/_x_accel_redirect/home/galaxy/galaxy-dist/database/files/000/dataset_4.dat

The dataset files are definitely present on the server and resides on
galaxy's database files directory (e.g. /database/files/000).

I can load and view in the browser any dataset that has 1MB in size, at
least those ones produced from the Galaxy 101 tutorial.

Any suggestion is appreciated.

Regards,

Jerico
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