Local Galaxy Instance MarkupSafe error
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
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. 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
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
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 <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
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
participants (3)
-
Jerico Nico De Leon Revote -
Mickael ESCUDERO -
Nate Coraor