Peter,

Can you confirm that you are running 10639:8045e137464f or later when this problem occurs? Fabric was upgraded in 10638, and the paramiko egg was added in 10639.

   --Dave B.

On 09/24/2013 12:21 PM, Peter Cock wrote:
Hmm.

This error message is unhelpful, no hint of if this is a local configuration
error (like the egg paths) or remote (e.g. the Galaxy egg cache):

$ python ./scripts/fetch_eggs.py
Warning: paramiko (a dependent egg of Fabric) cannot be fetched

(Meanwhile working from the stable branch avoids this)

Peter


On Tue, Sep 24, 2013 at 5:08 PM, Dave Bouvier <d...@bx.psu.edu> wrote:
Peter,

We recently upgraded the Fabric egg, which now depends on paramiko. You
should be able to resolve this issue by running

python ./scripts/fetch_eggs.py

    --Dave B.


On 09/24/2013 11:42 AM, Peter Cock wrote:

Hi all,

Has something changed recently on galaxy-central with the fabric egg,
and a possible missing dependency?

$ ./run.sh
...
galaxy.jobs.handler INFO 2013-09-24 16:40:21,849 job handler stop queue
started
galaxy.jobs.handler INFO 2013-09-24 16:40:21,867 job handler queue started
galaxy.sample_tracking.external_service_types DEBUG 2013-09-24
16:40:21,870 Loaded external_service_type: Simple unknown sequencer
1.0.0
galaxy.sample_tracking.external_service_types DEBUG 2013-09-24
16:40:21,873 Loaded external_service_type: Applied Biosystems SOLiD
1.0.0
galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,899 Enabling
'data_admin' controller, class: DataAdmin
galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,903 Enabling
'requests_common' controller, class: RequestsCommon
galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,905 Enabling
'forms' controller, class: Forms
galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,974 Enabling
'workflow' controller, class: WorkflowController
galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,975 Enabling
'async' controller, class: ASync
galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,975 Enabling
'library' controller, class: Library
galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,982 Enabling
'data_manager' controller, class: DataManager
galaxy.web.framework.base DEBUG 2013-09-24 16:40:21,983 Enabling
'error' controller, class: Error
galaxy.web.framework.base DEBUG 2013-09-24 16:40:22,213 Enabling
'cloudlaunch' controller, class: CloudController
galaxy.eggs WARNING 2013-09-24 16:40:22,480 Warning: paramiko (a
dependent egg of Fabric) cannot be fetched
Traceback (most recent call last):
    File
"/mnt/galaxy/galaxy-central/eggs/Fabric-1.7.0-py2.6.egg/fabric/network.py",
line 24, in <module>
      import paramiko as ssh
ImportError: No module named paramiko

There was a problem importing our SSH library (see traceback above).
Please make sure all dependencies are installed and importable
...

Also what is this CloudController and can I turn it off instead?

Thanks,

Peter
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