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

2011-11-03 Thread Mickael ESCUDERO 
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
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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
   
   
   -- 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
  
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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
   -- next part --
   An HTML attachment was scrubbed...
   URL: 
  
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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
   
   
   -- 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

[galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-10-31 Thread Mickael ESCUDERO 
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
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Re: [galaxy-dev] Local Galaxy Instance MarkupSafe error

2011-10-27 Thread Nate Coraor 
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/

___
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and other Galaxy lists, please use the interface at:

  http://lists.bx.psu.edu/

[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
___
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:

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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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